Rna interference mediated treatment of alzheimer&#39;s disease using short interfering nucleic acid (sina)

ABSTRACT

This invention relates to compounds, compositions, and methods useful for modulating beta-secretase (BACE), amyloid precurson protein (APP), PIN-1, presenillin 1 (PS-1) and/or presenillin 2 (PS-2) gene expression using short interfering nucleic acid (siNA) molecules. This invention also relates to compounds, compositions, and methods useful for modulating the expression and activity of other genes involved in pathways of BACE, APP, PIN-1, PS-1 and/or PS-2 gene expression and/or activity by RNA interference (RNAi) using small nucleic acid molecules. In particular, the instant invention features small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), doublestranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules and methods used to modulate the expression of BACE, APP, PIN-1, PS-1 and/or PS-2 genes.

This application is a continuation-in-part of U.S. patent application Ser. No. 10/607,933, filed Jun. 27, 2003, which is a continuation-in-part of U.S. patent application Ser. No. 09/930,423, filed Aug. 15, 2001 and is also a continuation-in-part of International Patent Application No. PCT/US03/04710, filed Feb. 18, 2003, which is a continuation-in-part of U.S. patent application Ser. No. 10/205,309, filed Jul. 25, 2002. This application is also a continuation-in-part of International Patent Application No. PCT/US04/16390, filed May 24, 2004, which is a continuation-in-part of U.S. patent application Ser. No. 10/826,966, filed Apr. 16, 2004, which is continuation-in-part of U.S. patent application Ser. No. 10/757,803, filed Jan. 14, 2004, which is a continuation-in-part of U.S. patent application Ser. No. 10/720,448, filed Nov. 24, 2003, which is a continuation-in-part of U.S. patent application Ser. No. 10/693,059, filed Oct. 23, 2003, which is a continuation-in-part of U.S. patent application Ser. No. 10/444,853, filed May 23, 2003, which is a continuation-in-part of International Patent Application No. PCT/US03/05346, filed Feb. 20, 2003, and a continuation-in-part of International Patent Application No. PCT/US03/05028, filed Feb. 20, 2003, both of which claim the benefit of U.S. Provisional Application No. 60/358,580, filed Feb. 20, 2002, U.S. Provisional Application No. 60/363,124, filed Mar. 11, 2002, U.S. Provisional Application No. 60/386,782, filed Jun. 6, 2002, U.S. Provisional Application No. 60/406,784, filed Aug. 29, 2002, U.S. Provisional Application No. 60/408,378, filed Sep. 5, 2002, U.S. Provisional Application No. 60/409,293, filed Sep. 9, 2002, and U.S. Provisional Application No. 60/440,129, filed Jan. 15, 2003. This application is also a continuation-in-part of International Patent Application No. PCT/US04/13456, filed Apr. 30, 2004, which is a continuation of patent application Ser. No. 10/780,447, filed Feb. 13, 2004, which is a continuation-in-part of U.S. patent application Ser. No. 10/427,160, filed Apr. 30, 2003, which is a continuation-in-part of International Patent Application No. PCT/US02/15876, filed May 17, 2002, which claims the benefit of U.S. Provisional Application No. 60/362,016, filed Mar. 6, 2002, and U.S. Provisional Application No. 60/292,217, filed May 18, 2001. This application is also a continuation-in-part of U.S. patent application Ser. No. 10/727,780, filed Dec. 3, 2003. This application also claims the benefit of U.S. Provisional Application No. 60/543,480, filed Feb. 10, 2004. The instant application claims the benefit of all the listed applications, which are hereby incorporated by reference herein in their entireties, including the drawings.

FIELD OF THE INVENTION

The present invention relates to compounds, compositions, and methods for the study, diagnosis, and treatment of traits, diseases and conditions associated with Alzheimer's disease. The present invention is also directed to compounds, compositions, and methods relating to traits, diseases and conditions that respond to the modulation of expression and/or activity of genes involved in beta-secretase (BACE), amyloid precursor protein (APP), PIN-1, presenillin 1 (PS-1) and/or presenillin 2 (PS-2) gene expression pathways or other cellular processes that mediate the maintenance or development of such traits, diseases and conditions. Specifically, the invention relates to small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules capable of mediating RNA interference (RNAi) against beta-secretase (BACE), amyloid precursor protein (APP), PIN-1, presenillin 1 (PS-1) and/or presenillin 2 (PS-2) gene expression. Such small nucleic acid molecules are useful, for example, in providing compositions for treatment of traits, diseases and conditions that can respond to modulation of beta-secretase (BACE), amyloid precursor protein (APP), PIN-1, presenillin 1 (PS-1) and/or presenillin 2 (PS-2) gene expression in a subject, such as Alzheimer's disease or dementia.

BACKGROUND OF THE INVENTION

The following is a discussion of relevant art pertaining to RNAi. The discussion is provided only for understanding of the invention that follows. The summary is not an admission that any of the work described below is prior art to the claimed invention.

RNA interference refers to the process of sequence-specific post-transcriptional gene silencing in animals mediated by short interfering RNAs (siRNAs) (Zamore et al., 2000, Cell, 101, 25-33; Fire et al., 1998, Nature, 391, 806; Hamilton et al., 1999, Science, 286, 950-951; Lin et al., 1999, Nature, 402, 128-129; Sharp, 1999, Genes & Dev., 13:139-141; and Strauss, 1999, Science, 286, 886). The corresponding process in plants (Heifetz et al., International PCT Publication No. WO 99/61631) is commonly referred to as post-transcriptional gene silencing or RNA silencing and is also referred to as quelling in fungi. The process of post-transcriptional gene silencing is thought to be an evolutionarily-conserved cellular defense mechanism used to prevent the expression of foreign genes and is commonly shared by diverse flora and phyla (Fire et al., 1999, Trends Genet., 15, 358). Such protection from foreign gene expression may have evolved in response to the production of double-stranded RNAs (dsRNAs) derived from viral infection or from the random integration of transposon elements into a host genome via a cellular response that specifically destroys homologous single-stranded RNA or viral genomic RNA. The presence of dsRNA in cells triggers the RNAi response through a mechanism that has yet to be fully characterized. This mechanism appears to be different from other known mechanisms involving double stranded RNA-specific ribonucleases, such as the interferon response that results from dsRNA-mediated activation of protein kinase PKR and 2′,5′-oligoadenylate synthetase resulting in non-specific cleavage of mRNA by ribonuclease L (see for example U.S. Pat. Nos. 6,107,094; 5,898,031; Clemens et al., 1997, J. Interferon &Cytokine Res., 17, 503-524; Adah et al., 2001, Curr. Med. Chem., 8, 1189).

The presence of long dsRNAs in cells stimulates the activity of a ribonuclease III enzyme referred to as dicer (Bass, 2000, Cell, 101, 235; Zamore et al., 2000, Cell, 101, 25-33; Hammond et al., 2000, Nature, 404, 293). Dicer is involved in the processing of the dsRNA into short pieces of dsRNA known as short interfering RNAs (siRNAs) (Zamore et al., 2000, Cell, 101, 25-33; Bass, 2000, Cell, 101, 235; Berstein et al., 2001, Nature, 409, 363). Short interfering RNAs derived from dicer activity are typically about 21 to about 23 nucleotides in length and comprise about 19 base pair duplexes (Zamore et al., 2000, Cell, 101, 25-33; Elbashir et al., 2001, Genes Dev., 15, 188). Dicer has also been implicated in the excision of 21- and 22-nucleotide small temporal RNAs (stRNAs) from precursor RNA of conserved structure that are implicated in translational control (Hutvagner et al., 2001, Science, 293, 834). The RNAi response also features an endonuclease complex, commonly referred to as an RNA-induced silencing complex (RISC), which mediates cleavage of single-stranded RNA having sequence complementary to the antisense strand of the siRNA duplex. Cleavage of the target RNA takes place in the middle of the region complementary to the antisense strand of the siRNA duplex (Elbashir et al., 2001, Genes Dev., 15, 188).

RNAi has been studied in a variety of systems. Fire et al., 1998, Nature, 391, 806, were the first to observe RNAi in C. elegans. Bahramian and Zarbl, 1999, Molecular and Cellular Biology, 19, 274-283 and Wianny and Goetz, 1999, Nature Cell Biol., 2, 70, describe RNAi mediated by dsRNA in mammalian systems. Hammond et al., 2000, Nature, 404, 293, describe RNAi in Drosophila cells transfected with dsRNA. Elbashir et al., 2001, Nature, 411, 494 and Tuschl et al., International PCT Publication No. WO 01/75164, describe RNAi induced by introduction of duplexes of synthetic 21-nucleotide RNAs in cultured mammalian cells including human embryonic kidney and HeLa cells. Recent work in Drosophila embryonic lysates (Elbashir et al., 2001, EMBO J, 20, 6877 and Tuschl et al., International PCT Publication No. WO 01/75164) has revealed certain requirements for siRNA length, structure, chemical composition, and sequence that are essential to mediate efficient RNAi activity. These studies have shown that 21-nucleotide siRNA duplexes are most active when containing 3′-terminal dinucleotide overhangs. Furthermore, complete substitution of one or both siRNA strands with 2′-deoxy(2′-H) or 2′-O-methyl nucleotides abolishes RNAi activity, whereas substitution of the 3′-terminal siRNA overhang nucleotides with 2′-deoxy nucleotides (2′-H) was shown to be tolerated. Single mismatch sequences in the center of the siRNA duplex were also shown to abolish RNAi activity. In addition, these studies also indicate that the position of the cleavage site in the target RNA is defined by the 5′-end of the siRNA guide sequence rather than the 3′-end of the guide sequence (Elbashir et al., 2001, EMBO J., 20, 6877). Other studies have indicated that a 5′-phosphate on the target-complementary strand of a siRNA duplex is required for siRNA activity and that ATP is utilized to maintain the 5′-phosphate moiety on the siRNA (Nykanen et al., 2001, Cell, 107, 309).

Studies have shown that replacing the 3′-terminal nucleotide overhanging segments of a 21-mer siRNA duplex having two-nucleotide 3′-overhangs with deoxyribonucleotides does not have an adverse effect on RNAi activity. Replacing up to four nucleotides on each end of the siRNA with deoxyribonucleotides has been reported to be well tolerated, whereas complete substitution with deoxyribonucleotides results in no RNAi activity (Elbashir et al., 2001, EMBO J., 20, 6877 and Tuschl et al., International PCT Publication No. WO 01/75164). In addition, Elbashir et al., supra, also report that substitution of siRNA with 2′-O-methyl nucleotides completely abolishes RNAi activity. Li et al., International PCT Publication No. WO 00/44914, and Beach et al., International PCT Publication No. WO 01/68836 preliminarily suggest that siRNA may include modifications to either the phosphate-sugar backbone or the nucleoside to include at least one of a nitrogen or sulfur heteroatom, however, neither application postulates to what extent such modifications would be tolerated in siRNA molecules, nor provides any further guidance or examples of such modified siRNA. Kreutzer et al., Canadian Patent Application No. 2,359,180, also describe certain chemical modifications for use in dsRNA constructs in order to counteract activation of double-stranded RNA-dependent protein kinase PKR, specifically 2′-amino or 2′-O-methyl nucleotides, and nucleotides containing a 2′-O or 4′-C methylene bridge. However, Kreutzer et al. similarly fails to provide examples or guidance as to what extent these modifications would be tolerated in dsRNA molecules.

Parrish et al., 2000, Molecular Cell, 6, 1077-1087, tested certain chemical modifications targeting the unc-22 gene in C. elegans using long (>25 nt) siRNA transcripts. The authors describe the introduction of thiophosphate residues into these siRNA transcripts by incorporating thiophosphate nucleotide analogs with T7 and T3 RNA polymerase and observed that RNAs with two phosphorothioate modified bases also had substantial decreases in effectiveness as RNAi. Further, Parrish et al. reported that phosphorothioate modification of more than two residues greatly destabilized the RNAs in vitro such that interference activities could not be assayed. Id. at 1081. The authors also tested certain modifications at the 2′-position of the nucleotide sugar in the long siRNA transcripts and found that substituting deoxynucleotides for ribonucleotides produced a substantial decrease in interference activity, especially in the case of Uridine to Thymidine and/or Cytidine to deoxy-Cytidine substitutions. Id. In addition, the authors tested certain base modifications, including substituting, in sense and antisense strands of the siRNA, 4-thiouracil, 5-bromouracil, 5-iodouracil, and 3-(aminoallyl)uracil for uracil, and inosine for guanosine. Whereas 4-thiouracil and 5-bromouracil substitution appeared to be tolerated, Parrish reported that inosine produced a substantial decrease in interference activity when incorporated in either strand. Parrish also reported that incorporation of 5-iodouracil and 3-(aminoallyl)uracil in the antisense strand resulted in a substantial decrease in RNAi activity as well.

The use of longer dsRNA has been described. For example, Beach et al., International PCT Publication No. WO 01/68836, describes specific methods for attenuating gene expression using endogenously-derived dsRNA. Tuschl et al., International PCT Publication No. WO 01/75164, describe a Drosophila in vitro RNAi system and the use of specific siRNA molecules for certain functional genomic and certain therapeutic applications; although Tuschl, 2001, Chem. Biochem., 2, 239-245, doubts that RNAi can be used to cure genetic diseases or viral infection due to the danger of activating interferon response. Li et al., International PCT Publication No. WO 00/44914, describe the use of specific long (141 bp-488 bp) enzymatically synthesized or vector expressed dsRNAs for attenuating the expression of certain target genes. Zernicka-Goetz et al., International PCT Publication No. WO 01/36646, describe certain methods for inhibiting the expression of particular genes in mammalian cells using certain long (550 bp-714 bp), enzymatically synthesized or vector expressed dsRNA molecules. Fire et al., International PCT Publication No. WO 99/32619, describe particular methods for introducing certain long dsRNA molecules into cells for use in inhibiting gene expression in nematodes. Plaetinck et al., International PCT Publication No. WO 00/01846, describe certain methods for identifying specific genes responsible for conferring a particular phenotype in a cell using specific long dsRNA molecules. Mello et al., International PCT Publication No. WO 01/29058, describe the identification of specific genes involved in dsRNA-mediated RNAi. Pachuck et al., International PCT Publication No. WO 00/63364, describe certain long (at least 200 nucleotide) dsRNA constructs. Deschamps Depaillette et al., International PCT Publication No. WO 99/07409, describe specific compositions consisting of particular dsRNA molecules combined with certain anti-viral agents. Waterhouse et al., International PCT Publication No. 99/53050 and 1998, PNAS, 95, 13959-13964, describe certain methods for decreasing the phenotypic expression of a nucleic acid in plant cells using certain dsRNAs. Driscoll et al., International PCT Publication No. WO 01/49844, describe specific DNA expression constructs for use in facilitating gene silencing in targeted organisms.

Others have reported on various RNAi and gene-silencing systems. For example, Parrish et al., 2000, Molecular Cell, 6, 1077-1087, describe specific chemically-modified dsRNA constructs targeting the unc-22 gene of C. elegans. Grossniklaus, International PCT Publication No. WO 01/38551, describes certain methods for regulating polycomb gene expression in plants using certain dsRNAs. Churikov et al., International PCT Publication No. WO 01/42443, describe certain methods for modifying genetic characteristics of an organism using certain dsRNAs. Cogoni et al., International PCT Publication No. WO 01/53475, describe certain methods for isolating a Neurospora silencing gene and uses thereof. Reed et al., International PCT Publication No. WO 01/68836, describe certain methods for gene silencing in plants. Honer et al., International PCT Publication No. WO 01/7944, describe certain methods of drug screening using transgenic nematodes as Parkinson's Disease models using certain dsRNAs. Deak et al., International PCT Publication No. WO 01/72774, describe certain Drosophila-derived gene products that may be related to RNAi in Drosophila. Arndt et al., International PCT Publication No. WO 01/92513 describe certain methods for mediating gene suppression by using factors that enhance RNAi. Tuschl et al., International PCT Publication No. WO 02/44321, describe certain synthetic siRNA constructs. Pachuk et al., International PCT Publication No. WO 00/63364, and Satishchandran et al., International PCT Publication No. WO 01/04313, describe certain methods and compositions for inhibiting the function of certain polynucleotide sequences using certain long (over 250 bp), vector expressed dsRNAs. Echeverri et al., International PCT Publication No. WO 02/38805, describe certain C. elegans genes identified via RNAi. Kreutzer et al., International PCT Publications Nos. WO 02/055692, WO 02/055693, and EP 1144623 B1 describes certain methods for inhibiting gene expression using dsRNA. Graham et al., International PCT Publications Nos. WO 99/49029 and WO 01/70949, and AU 4037501 describe certain vector expressed siRNA molecules. Fire et al., U.S. Pat. No. 6,506,559, describe certain methods for inhibiting gene expression in vitro using certain long dsRNA (299 bp-1033 bp) constructs that mediate RNAi. Martinez et al., 2002, Cell, 110, 563-574, describe certain single stranded siRNA constructs, including certain 5′-phosphorylated single stranded siRNAs that mediate RNA interference in Hela cells. Harborth et al., 2003, Antisense & Nucleic Acid Drug Development, 13, 83-105, describe certain chemically and structurally modified siRNA molecules. Chiu and Rana, 2003, RNA, 9, 1034-1048, describe certain chemically and structurally modified siRNA molecules. Woolf et al., International PCT Publication Nos. WO 03/064626 and WO 03/064625 describe certain chemically modified dsRNA constructs.

McSwiggen et al., International PCT Publication No. WO 01/16312, describes nucleic acid mediated inhibition of BACE, PS-1, and PS-2 expression.

SUMMARY OF THE INVENTION

This invention relates to compounds, compositions, and methods useful for modulating the expression of genes associated with the maintenance or development of Alzheimer's disease and/or dementia, for example, beta-secretase (BACE), amyloid precursor protein (APP), PIN-1, presenillin 1 (PS-1) and/or presenillin 2 (PS-2) gene expression using short interfering nucleic acid (siNA) molecules. This invention also relates to compounds, compositions, and methods useful for modulating the expression and activity of other genes involved in pathways of BACE, APP, PIN-1, PS-1 and/or PS-2 gene expression and/or activity by RNA interference (RNAi) using small nucleic acid molecules. In particular, the instant invention features small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (mRNA), and short hairpin RNA (shRNA) molecules and methods used to modulate the expression of BACE, APP, PIN-1, PS-1 and/or PS-2 genes or other genes associated with the maintenance or development of Alzheimer's disease and/or dementia.

A siNA of the invention can be unmodified or chemically-modified. A siNA of the instant invention can be chemically synthesized, expressed from a vector or enzymatically synthesized. The instant invention also features various chemically-modified synthetic short interfering nucleic acid (siNA) molecules capable of modulating BACE, APP, PIN-1, PS-1 and/or PS-2 gene expression or activity in cells by RNA interference (RNAi). The use of chemically-modified siNA improves various properties of native siNA molecules through increased resistance to nuclease degradation in vivo and/or through improved cellular uptake. Further, contrary to earlier published studies, siNA having multiple chemical modifications retains its RNAi activity. The siNA molecules of the instant invention provide useful reagents and methods for a variety of therapeutic, diagnostic, target validation, genomic discovery, genetic engineering, and pharmacogenomic applications.

In one embodiment, the invention features one or more siNA molecules and methods that independently or in combination modulate the expression of BACE, APP, PIN-1, PS-1 and/or PS-2 genes encoding proteins, such as proteins comprising BACE, APP, PIN-1, PS-1 and/or PS-2 associated with the maintenance and/or development of Alzheimer's disease and other neurodegenerative disorders or conditions such as dementia and stroke/cardiovascular accident (CVA), such as genes encoding sequences comprising those sequences referred to by GenBank Accession Nos. shown in Table I, referred to herein generally as BACE, APP, PIN-1, PS-1 and/or PS-2. The description below of the various aspects and embodiments of the invention is provided with reference to exemplary BACE gene referred to herein as BACE. However, the various aspects and embodiments are also directed to other BACE genes, such as BACE homolog genes, transcript variants and polymorphisms (e.g., single nucleotide polymorphism, (SNPs)) associated with certain BACE genes. As such, the various aspects and embodiments are also directed to other genes which express other BACE related proteins or other proteins associated with Alzheimer's disease, such as APP, PIN-1, PS-1 and/or PS-2, including mutant genes and splice variants thereof. The various aspects and embodiments are also directed to other genes that are involved in BACE, APP, PIN-1, PS-1 and/or PS-2 mediated pathways of signal transduction or gene expression that are involved, for example, in the progression, development, or maintenance of disease (e.g., Alzheimer's disease). These additional genes can be analyzed for target sites using the methods described for BACE genes herein. Thus, the modulation of other genes and the effects of such modulation of the other genes can be performed, determined, and measured as described herein.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a BACE gene, wherein said siNA molecule comprises about 18 to about 21 base pairs.

In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that directs cleavage of BACE RNA via RNA interference (RNAi), wherein the double stranded siNA molecule comprises a first and a second strand, each strand of the siNA molecule is about 18 to about 23 nucleotides in length, the first strand of the siNA molecule comprises nucleotide sequence having sufficient complementarity to the BACE RNA for the siNA molecule to direct cleavage of the BACE RNA via RNA interference, and the second strand of said siNA molecule comprises nucleotide sequence that is complementary to the first strand.

In one embodiment, the invention features a chemically synthesized double stranded short interfering nucleic acid (siNA) molecule that directs cleavage of a BACE RNA via RNA interference (RNAi), wherein each strand of the siNA molecule is about 18 to about 23 nucleotides in length; and one strand of the sNA molecule comprises nucleotide sequence having sufficient complementarity to the BACE RNA for the siNA molecule to direct cleavage of the BACE RNA via RNA interference.

In one embodiment, the invention features a siNA molecule that down-regulates expression of a BACE gene, for example, wherein the BACE gene comprises BACE encoding sequence. In one embodiment, the invention features a siNA molecule that down-regulates expression of a BACE gene, for example, wherein the BACE gene comprises BACE non-coding sequence or regulatory elements involved in BACE gene expression.

In one embodiment, a siNA of the invention is used to inhibit the expression of BACE genes or a BACE gene family, wherein the genes or gene family sequences share sequence homology. Such homologous sequences can be identified as is known in the art, for example using sequence alignments. siNA molecules can be designed to target such homologous sequences, for example using perfectly complementary sequences or by incorporating non-canonical base pairs, for example mismatches and/or wobble base pairs, that can provide additional target sequences. In instances where mismatches are identified, non-canonical base pairs (for example, mismatches and/or wobble bases) can be used to generate siNA molecules that target more than one gene sequence. In a non-limiting example, non-canonical base pairs such as UU and CC base pairs are used to generate siNA molecules that are capable of targeting sequences for differing BACE targets that share sequence homology. As such, one advantage of using siNAs of the invention is that a single siNA can be designed to include nucleic acid sequence that is complementary to the nucleotide sequence that is conserved between the homologous genes. In this approach, a single siNA can be used to inhibit expression of more than one gene instead of using more than one siNA molecule to target the different genes.

In one embodiment, the invention features a siNA molecule having RNAi activity against BACE RNA, wherein the siNA molecule comprises a sequence complementary to any RNA having BACE encoding sequence, such as those sequences having GenBank Accession Nos. shown in Table I. In another embodiment, the invention features a siNA molecule having RNAi activity against BACE RNA, wherein the siNA molecule comprises a sequence complementary to an RNA having variant BACE encoding sequence, for example other mutant BCAE genes not shown in Table I but known in the art to be associated with the maintenance and/or development of Alzheimer's disease and/or dementia. Chemical modifications as shown in Tables III and IV or otherwise described herein can be applied to any siNA construct of the invention. In another embodiment, a siNA molecule of the invention includes a nucleotide sequence that can interact with nucleotide sequence of a BACE gene and thereby mediate silencing of BACE gene expression, for example, wherein the siNA mediates regulation of BACE gene expression by cellular processes that modulate the chromatin structure or methylation patterns of the BACE gene and prevent transcription of the BACE gene.

In one embodiment, siNA molecules of the invention are used to down regulate or inhibit the expression of BACE proteins arising from BACE haplotype polymorphisms that are associated with a disease or condition, (e.g., Alzheimer's disease and other neurodegenerative disorders or conditions such as dementia and stroke/cardiovascular accident (CVA)). Analysis of BACE genes, or BACE protein or RNA levels can be used to identify subjects with such polymorphisms or those subjects who are at risk of developing traits, conditions, or diseases described herein. These subjects are amenable to treatment, for example, treatment with siNA molecules of the invention and any other composition useful in treating diseases related to BACE gene expression. As such, analysis of BACE protein or RNA levels can be used to determine treatment type and the course of therapy in treating a subject. Monitoring of BACE protein or RNA levels can be used to predict treatment outcome and to determine the efficacy of compounds and compositions that modulate the level and/or activity of certain BACE proteins associated with a trait, condition, or disease.

In one embodiment of the invention a siNA molecule comprises an antisense strand comprising a nucleotide sequence that is complementary to a nucleotide sequence or a portion thereof encoding a BACE protein. The siNA further comprises a sense strand, wherein said sense strand comprises a nucleotide sequence of a BACE gene or a portion thereof.

In another embodiment, a siNA molecule comprises an antisense region comprising a nucleotide sequence that is complementary to a nucleotide sequence encoding a BACE protein or a portion thereof. The sNA molecule further comprises a sense region, wherein said sense region comprises a nucleotide sequence of a BACE gene or a portion thereof.

In another embodiment, the invention features a siNA molecule comprising a nucleotide sequence in the antisense region of the siNA molecule that is complementary to a nucleotide sequence or portion of sequence of a BACE gene. In another embodiment, the invention features a siNA molecule comprising a region, for example, the antisense region of the siNA construct, complementary to a sequence comprising a BACE gene sequence or a portion thereof.

In one embodiment, the antisense region of BACE siNA constructs comprises a sequence complementary to sequence having any of SEQ ID NOs. 399-723, 1471-1478, 1591-1598, 1607-1614, 1623-1630, 1639-1646, 1655-1662, 1687, or 1689. In one embodiment, the antisense region of BACE constructs comprises sequence having any of SEQ ID NOs. 724-1048, 1599-1606, 1615-1622, 1631-1638, 1647-1654, 1663-1686, 1688, 1690, 1884, 1886, 1888, 1891, 1893, 1895, 1897, or 1900. In another embodiment, the sense region of BACE constructs comprises sequence having any of SEQ ID NOs. 399-723, 1471-1478, 1591-1598, 1607-1614, 1623-1630, 1639-1646, 1655-1662, 1687, 1689, 1883, 1885, 1887, 1889, 1890, 1892, 1894, 1896, 1898, or 1899.

In one embodiment, the antisense region of APP siNA constructs comprises a sequence complementary to sequence having any of SEQ ID NOs. 1-199, 1463-1470, 1495-1502, 1511-1518, 1527-1534, 1543-1550, or 1559-1566. In one embodiment, the antisense region of APP constructs comprises sequence having any of SEQ ID NOs. 200-398, 1503-1510, 1519-1526, 1535-1542, 1551-1558, 1567-1590, 1884, 1886, 1888, or 1891. In another embodiment, the sense region of APP constructs comprises sequence having any of SEQ ID NOs. 1-199, 1463-1470, 1495-1502, 1511-1518, 1527-1534, 1543-1550, 1559-1566, 1883, 1885, 1887, 1889, or 1890.

In one embodiment, the antisense region of PSEN1 siNA constructs comprises a sequence complementary to sequence having any of SEQ ID NOs. 1049-1131, 1479-1486, 1691-1698, 1707-1714, 1723-1730, 1739-1746, 1755-1762. In one embodiment, the antisense region of PSEN1 constructs comprises sequence having any of SEQ ID NOs. 1132-1214, 1699-1706, 1715-1722, 1731-1738, 1747-1754, 1763-1786, 1884, 1886, 1888, or 1891. In another embodiment, the sense region of PSEN1 constructs comprises sequence having any of SEQ ID NOs. 1049-1131, 1479-1486, 1691-1698, 1707-1714, 1723-1730, 1739-1746, 1755-1762, 1883, 1885, 1887, 1889, or 1890.

In one embodiment, the antisense region of PSEN2 siNA constructs comprises a sequence complementary to sequence having any of SEQ ID NOs. 1215-1338, 1487-1494, 1787-1794, 1803-1810, 1819-1826, 1835-1842, 1851-1858. In one embodiment, the antisense region of PSEN2 constructs comprises sequence having any of SEQ ID NOs. 1339-1462, 1795-1802, 1811-1818, 1827-1834, 1843-1850, 1859-1882, 1884, 1886, 1888, or 1891. In another embodiment, the sense region of PSEN2 constructs comprises sequence having any of SEQ ID NOs. SEQ ID NOs. 1215-1338, 1487-1494, 1787-1794, 1803-1810, 1819-1826, 1835-1842, 1851-1858, 1883, 1885, 1887, 1889, or 1890.

In one embodiment, a siNA molecule of the invention comprises any of SEQ ID NOs. 1-1900. The sequences shown in SEQ ID NOs: 1-1900 are not limiting. A siNA molecule of the invention can comprise any contiguous BACE sequence (e.g., about 18 to about 25, or about 18, 19, 20, 21, 22, 23, 24, or 25 contiguous BACE nucleotides).

In yet another embodiment, the invention features a siNA molecule comprising a sequence, for example, the antisense sequence of the siNA construct, complementary to a sequence or portion of sequence comprising sequence represented by GenBank Accession Nos. shown in Table I. Chemical modifications in Tables m and IV and described herein can be applied to any siNA construct of the invention.

In one embodiment of the invention a siNA molecule comprises an antisense strand having about 18 to about 29 (e.g., about 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29) nucleotides, wherein the antisense strand is complementary to a RNA sequence encoding a BACE protein, and wherein said siNA further comprises a sense strand having about 18 to about 29 (e.g., about 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29) nucleotides, and wherein said sense strand and said antisense strand are distinct nucleotide sequences with at least about 18 complementary nucleotides.

In another embodiment of the invention a siNA molecule of the invention comprises an antisense region having about 18 to about 29 (e.g., about 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29) nucleotides, wherein the antisense region is complementary to a RNA sequence encoding a BACE protein, and wherein said siNA further comprises a sense region having about 18 to about 29 (e.g., about 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29) nucleotides, wherein said sense region and said antisense region comprise a linear molecule with at least about 19 complementary nucleotides.

In one embodiment, a siNA molecule of the invention has RNAi activity that modulates expression of RNA encoded by a BACE gene. Because BACE genes can share some degree of sequence homology with each other, siNA molecules can be designed to target a class of BACE genes or alternately specific BACE genes (e.g., polymorphic variants) by selecting sequences that are either shared amongst different BACE targets or alternatively that are unique for a specific BACE target. Therefore, in one embodiment, the siNA molecule can be designed to target conserved regions of BACE RNA sequences having homology among several BACE gene variants so as to target a class of BACE genes with one siNA molecule. Accordingly, in one embodiment, the siNA molecule of the invention modulates the expression of one or both BACE alleles in a subject. In another embodiment, the siNA molecule can be designed to target a sequence that is unique to a specific BACE RNA sequence (e.g., a single BACE allele or BACE single nucleotide polymorphism (SNP)) due to the high degree of specificity that the siNA molecule requires to mediate RNAi activity.

In one embodiment, nucleic acid molecules of the invention that act as mediators of the RNA interference gene silencing response are double-stranded nucleic acid molecules. In another embodiment, the siNA molecules of the invention consist of duplex nucleic acid molecules containing about 18 base pairs between oligonucleotides comprising about 18 to about 25 (e.g., about 18, 19, 20, 21, 22, 23, 24, or 25) nucleotides. In yet another embodiment, siNA molecules of the invention comprise duplex nucleic acid molecules with overhanging ends of about about 1 to about 3 (e.g., about 1, 2, or 3) nucleotides, for example, about 21-nucleotide duplexes with about 18 base pairs and 3′-terminal mononucleotide, dinucleotide, or trinucleotide overhangs.

In one embodiment, the invention features one or more chemically-modified siNA constructs having specificity for BACE expressing nucleic acid molecules, such as RNA encoding a BACE protein. In one embodiment, the invention features a RNA based siNA molecule (e.g., a siNA comprising 2′-OH nucleotides) having specificity for BACE expressing nucleic acid molecules that includes one or more chemical modifications described herein. Non-limiting examples of such chemical modifications include without limitation phosphorothioate internucleotide linkages, 2′-deoxyribonucleotides, 2′-O-methyl ribonucleotides, 2′-deoxy-2′-fluoro ribonucleotides, “universal base” nucleotides, “acyclic” nucleotides, 5-C-methyl nucleotides, and terminal glyceryl and/or inverted deoxy abasic residue incorporation. These chemical modifications, when used in various siNA constructs, (e.g., RNA based siNA constructs), are shown to preserve RNAi activity in cells while at the same time, dramatically increasing the serum stability of these compounds. Furthermore, contrary to the data published by Parrish et al., supra, applicant demonstrates that multiple (greater than one) phosphorothioate substitutions are well-tolerated and confer substantial increases in serum stability for modified siNA constructs.

In one embodiment, a siNA molecule of the invention comprises modified nucleotides while maintaining the ability to mediate RNAi. The modified nucleotides can be used to improve in vitro or in vivo characteristics such as stability, activity, and/or bioavailability. For example, a siNA molecule of the invention can comprise modified nucleotides as a percentage of the total number of nucleotides present in the siNA molecule. As such, a siNA molecule of the invention can generally comprise about 5% to about 100% modified nucleotides (e.g., about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% modified nucleotides). The actual percentage of modified nucleotides present in a given siNA molecule will depend on the total number of nucleotides present in the siNA. If the siNA molecule is single stranded, the percent modification can be based upon the total number of nucleotides present in the single stranded siNA molecules. Likewise, if the siNA molecule is double stranded, the percent modification can be based upon the total number of nucleotides present in the sense strand, antisense strand, or both the sense and antisense strands.

One aspect of the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a BACE gene. In one embodiment, the double stranded siNA molecule comprises one or more chemical modifications and each strand of the double-stranded siNA is about 21 nucleotides long. In one embodiment, the double-stranded siNA molecule does not contain any ribonucleotides. In another embodiment, the double-stranded siNA molecule comprises one or more ribonucleotides. In one embodiment, each strand of the double-stranded siNA molecule comprises about 18 to about 29 (e.g., about 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29) nucleotides, wherein each strand comprises about 18 nucleotides that are complementary to the nucleotides of the other strand. In one embodiment, one of the strands of the double-stranded siNA molecule comprises a nucleotide sequence that is complementary to a nucleotide sequence or a portion thereof of the BACE gene, and the second strand of the double-stranded siNA molecule comprises a nucleotide sequence substantially similar to the nucleotide sequence of the BACE gene or a portion thereof.

In another embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a BACE gene comprising an antisense region, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of the BACE gene or a portion thereof, and a sense region, wherein the sense region comprises a nucleotide sequence substantially similar to the nucleotide sequence of the BACE gene or a portion thereof. In one embodiment, the antisense region and the sense region each comprise about 18 to about 23 (e.g. about 18, 19, 20, 21, 22, or 23) nucleotides, wherein the antisense region comprises about 18 nucleotides that are complementary to nucleotides of the sense region.

In another embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a BACE gene comprising a sense region and an antisense region, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by the BACE gene or a portion thereof and the sense region comprises a nucleotide sequence that is complementary to the antisense region.

In one embodiment, a siNA molecule of the invention comprises blunt ends, i.e., ends that do not include any overhanging nucleotides. For example, a siNA molecule comprising modifications described herein (e.g., comprising nucleotides having Formulae I-VII or siNA constructs comprising “Stab 00”-“Stab 25” (Table IV) or any combination thereof (see Table IV)) and/or any length described herein can comprise blunt ends or ends with no overhanging nucleotides.

In one embodiment, any siNA molecule of the invention can comprise one or more blunt ends, i.e. where a blunt end does not have any overhanging nucleotides. In one embodiment, the blunt ended siNA molecule has a number of base pairs equal to the number of nucleotides present in each strand of the siNA molecule. In another embodiment, the siNA molecule comprises one blunt end, for example wherein the 5′-end of the antisense strand and the 3′-end of the sense strand do not have any overhanging nucleotides. In another example, the siNA molecule comprises one blunt end, for example wherein the 3′-end of the antisense strand and the 5′-end of the sense strand do not have any overhanging nucleotides. In another example, a siNA molecule comprises two blunt ends, for example wherein the 3′-end of the antisense strand and the 5′-end of the sense strand as well as the 5′-end of the antisense strand and 3′-end of the sense strand do not have any overhanging nucleotides. A blunt ended siNA molecule can comprise, for example, from about 18 to about 30 nucleotides (e.g., about 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides). Other nucleotides present in a blunt ended siNA molecule can comprise, for example, mismatches, bulges, loops, or wobble base pairs to modulate the activity of the siNA molecule to mediate RNA interference.

By “blunt ends” is meant symmetric termini or termini of a double stranded siNA molecule having no overhanging nucleotides. The two strands of a double stranded siNA molecule align with each other without over-hanging nucleotides at the termini. For example, a blunt ended siNA construct comprises terminal nucleotides that are complementary between the sense and antisense regions of the siNA molecule.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (sNA) molecule that down-regulates expression of a BACE gene, wherein the siNA molecule is assembled from two separate oligonucleotide fragments wherein one fragment comprises the sense region and the second fragment comprises the antisense region of the siNA molecule. The sense region can be connected to the antisense region via a linker molecule, such as a polynucleotide linker or a non-nucleotide linker.

In one embodiment, the invention features double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a BACE gene, wherein the siNA molecule comprises about 18 to about 21 base pairs, and wherein each strand of the siNA molecule comprises one or more chemical modifications. In another embodiment, one of the strands of the double-stranded siNA molecule comprises a nucleotide sequence that is complementary to a nucleotide sequence of a BACE gene or a portion thereof, and the second strand of the double-stranded siNA molecule comprises a nucleotide sequence substantially similar to the nucleotide sequence or a portion thereof of the BACE gene. In another embodiment, one of the strands of the double-stranded siNA molecule comprises a nucleotide sequence that is complementary to a nucleotide sequence of a BACE gene or portion thereof, and the second strand of the double-stranded siNA molecule comprises a nucleotide sequence substantially similar to the nucleotide sequence or portion thereof of the BACE gene. In another embodiment, each strand of the siNA molecule comprises about 18 to about 23 nucleotides, and each strand comprises at least about 18 nucleotides that are complementary to the nucleotides of the other strand. The BACE gene can comprise, for example, sequences referred to in Table I.

In one embodiment, a siNA molecule of the invention comprises no ribonucleotides. In another embodiment, a siNA molecule of the invention comprises ribonucleotides.

In one embodiment, a siNA molecule of the invention comprises an antisense region comprising a nucleotide sequence that is complementary to a nucleotide sequence of a BACE gene or a portion thereof, and the siNA further comprises a sense region comprising a nucleotide sequence substantially similar to the nucleotide sequence of the BACE gene or a portion thereof. In another embodiment, the antisense region and the sense region each comprise about 18 to about 23 nucleotides and the antisense region comprises at least about 18 nucleotides that are complementary to nucleotides of the sense region. The BACE gene can comprise, for example, sequences referred to in Table I.

In one embodiment, a siNA molecule of the invention comprises a sense region and an antisense region, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by a BACE gene, or a portion thereof, and the sense region comprises a nucleotide sequence that is complementary to the antisense region. In one embodiment, the siNA molecule is assembled from two separate oligonucleotide fragments, wherein one fragment comprises the sense region and the second fragment comprises the antisense region of the siNA molecule. In another embodiment, the sense region is connected to the antisense region via a linker molecule. In another embodiment, the sense region is connected to the antisense region via a linker molecule, such as a nucleotide or non-nucleotide linker. The BACE gene can comprise, for example, sequences referred in to Table I.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a BACE gene comprising a sense region and an antisense region, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by the BACE gene or a portion thereof and the sense region comprises a nucleotide sequence that is complementary to the antisense region, and wherein the siNA molecule has one or more modified pyrimidine and/or purine nucleotides. In one embodiment, the pyrimidine nucleotides in the sense region are 2′-O-methyl pyrimidine nucleotides or 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-deoxy purine nucleotides. In another embodiment, the pyrimidine nucleotides in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-O-methyl purine nucleotides. In another embodiment, the pyrimidine nucleotides in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-deoxy purine nucleotides. In one embodiment, the pyrimidine nucleotides in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the antisense region are 2′-O-methyl or 2′-deoxy purine nucleotides. In another embodiment of any of the above-described siNA molecules, any nucleotides present in a non-complementary region of the sense strand (e.g. overhang region) are 2′-deoxy nucleotides.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a BACE gene, wherein the siNA molecule is assembled from two separate oligonucleotide fragments wherein one fragment comprises the sense region and the second fragment comprises the antisense region of the siNA molecule, and wherein the fragment comprising the sense region includes a terminal cap moiety at the 5′-end, the 3′-end, or both of the 5′ and 3′ ends of the fragment. In one embodiment, the terminal cap moiety is an inverted deoxy abasic moiety or glyceryl moiety. In one embodiment, each of the two fragments of the siNA molecule comprise about 21 nucleotides.

In one embodiment, the invention features a siNA molecule comprising at least one modified nucleotide, wherein the modified nucleotide is a 2′-deoxy-2′-fluoro nucleotide. The siNA can be, for example, of length between about 12 and about 36 nucleotides. In one embodiment, all pyrimidine nucleotides present in the siNA are 2′-deoxy-2′-fluoro pyrimidine nucleotides. In one embodiment, the modified nucleotides in the siNA include at least one 2′-deoxy-2′-fluoro cytidine or 2′-deoxy-2′-fluoro uridine nucleotide. In another embodiment, the modified nucleotides in the siNA include at least one 2′-fluoro cytidine and at least one 2′-deoxy-2′-fluoro uridine nucleotides. In one embodiment, all uridine nucleotides present in the siNA are 2′-deoxy-2′-fluoro uridine nucleotides. In one embodiment, all cytidine nucleotides present in the siNA are 2′-deoxy-2′-fluoro cytidine nucleotides. In one embodiment, all adenosine nucleotides present in the siNA are 2′-deoxy-2′-fluoro adenosine nucleotides. In one embodiment, all guanosine nucleotides present in the siNA are 2′-deoxy-2′-fluoro guanosine nucleotides. The siNA can further comprise at least one modified internucleotidic linkage, such as phosphorothioate linkage. In one embodiment, the 2′-deoxy-2′-fluoronucleotides are present at specifically selected locations in the siNA that are sensitive to cleavage by ribonucleases, such as locations having pyrimidine nucleotides.

In one embodiment, the invention features a method of increasing the stability of a siNA molecule against cleavage by ribonucleases comprising introducing at least one modified nucleotide into the siNA molecule, wherein the modified nucleotide is a 2′-deoxy-2′-fluoro nucleotide. In one embodiment, all pyrimidine nucleotides present in the siNA are 2′-deoxy-2′-fluoro pyrimidine nucleotides. In one embodiment, the modified nucleotides in the siNA include at least one 2′-deoxy-2′-fluoro cytidine or 2′-deoxy-2′-fluoro uridine nucleotide. In another embodiment, the modified nucleotides in the siNA include at least one 2′-fluoro cytidine and at least one 2′-deoxy-2′-fluoro uridine nucleotides. In one embodiment, all uridine nucleotides present in the siNA are 2′-deoxy-2′-fluoro uridine nucleotides. In one embodiment, all cytidine nucleotides present in the siNA are 2′-deoxy-2′-fluoro cytidine nucleotides. In one embodiment, all adenosine nucleotides present in the siNA are 2′-deoxy-2′-fluoro adenosine nucleotides. In one embodiment, all guanosine nucleotides present in the siNA are 2′-deoxy-2′-fluoro guanosine nucleotides. The siNA can further comprise at least one modified internucleotidic linkage, such as phosphorothioate linkage. In one embodiment, the 2′-deoxy-2′-fluoronucleotides are present at specifically selected locations in the siNA that are sensitive to cleavage by ribonucleases, such as locations having pyrimidine nucleotides.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a BACE gene comprising a sense region and an antisense region, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by the BACE gene or a portion thereof and the sense region comprises a nucleotide sequence that is complementary to the antisense region, and wherein the purine nucleotides present in the antisense region comprise 2′-deoxy-purine nucleotides. In an alternative embodiment, the purine nucleotides present in the antisense region comprise 2′-O-methyl purine nucleotides. In either of the above embodiments, the antisense region can comprise a phosphorothioate internucleotide linkage at the 3′ end of the antisense region. Alternatively, in either of the above embodiments, the antisense region can comprise a glyceryl modification at the 3′ end of the antisense region. In another embodiment of any of the above-described siNA molecules, any nucleotides present in a non-complementary region of the antisense strand (e.g. overhang region) are 2′-deoxy nucleotides.

In one embodiment, the antisense region of a siNA molecule of the invention comprises sequence complementary to a portion of a BACE transcript having sequence unique to a particular BACE disease related allele, such as sequence comprising a single nucleotide polymorphism (SNP) associated with the disease specific allele. As such, the antisense region of a siNA molecule of the invention can comprise sequence complementary to sequences that are unique to a particular allele to provide specificity in mediating selective RNAi against the disease, condition, or trait related allele.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a BACE gene, wherein the siNA molecule is assembled from two separate oligonucleotide fragments wherein one fragment comprises the sense region and the second fragment comprises the antisense region of the siNA molecule. In another embodiment about 19 nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule and wherein at least two 3′ terminal nucleotides of each fragment of the siNA molecule are not base-paired to the nucleotides of the other fragment of the siNA molecule. In one embodiment, each of the two 3′ terminal nucleotides of each fragment of the siNA molecule is a 2′-deoxy-pyrimidine nucleotide, such as a 2′-deoxy-thymidine. In another embodiment, all 21 nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule. In another embodiment, about 19 nucleotides of the antisense region are base-paired to the nucleotide sequence or a portion thereof of the RNA encoded by the BACE gene. In another embodiment, about 21 nucleotides of the antisense region are base-paired to the nucleotide sequence or a portion thereof of the RNA encoded by the BACE gene. In any of the above embodiments, the 5′-end of the fragment comprising said antisense region can optionally includes a phosphate group.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits the expression of a BACE RNA sequence (e.g., wherein said target RNA sequence is encoded by a BACE gene involved in the BACE pathway), wherein the siNA molecule does not contain any ribonucleotides and wherein each strand of the double-stranded sNA molecule is about 21 nucleotides long. Examples of non-ribonucleotide containing siNA constructs are combinations of stabilization chemistries shown in Table IV in any combination of Sense/Antisense chemistries, such as Stab 7/8, Stab 7/11, Stab 8/8, Stab 18/8, Stab 18/11, Stab 12/13, Stab 7/13, Stab 18/13, Stab 7/19, Stab 8/19, Stab 18/19, Stab 7/20, Stab 8/20, or Stab 18/20.

In one embodiment, the invention features a chemically synthesized double stranded RNA molecule that directs cleavage of a BACE RNA via RNA interference, wherein each strand of said RNA molecule is about 21 to about 23 nucleotides in length; one strand of the RNA molecule comprises nucleotide sequence having sufficient complementarity to the BACE RNA for the RNA molecule to direct cleavage of the BACE RNA via RNA interference; and wherein at least one strand of the RNA molecule comprises one or more chemically modified nucleotides described herein, such as deoxynucleotides, 2′-O-methyl nucleotides, 2′-deoxy-2′-fluoro nucloetides, 2′-O-methoxyethyl nucleotides etc.

In one embodiment, the invention features a medicament comprising a siNA molecule of the invention.

In one embodiment, the invention features an active ingredient comprising a siNA molecule of the invention.

In one embodiment, the invention features the use of a double-stranded short interfering nucleic acid (siNA) molecule to down-regulate expression of a BACE gene, wherein the siNA molecule comprises one or more chemical modifications and each strand of the double-stranded siNA is about 18 to about 28 or more (e.g., about 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 or more) nucleotides long.

In one embodiment, the invention features the use of a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a BACE gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of BACE RNA or a portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a BACE gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of BACE RNA or a portion thereof, wherein the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a BACE gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of BACE RNA that encodes a protein or portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification. In one embodiment, each strand of the siNA molecule comprises about 18 to about 29 or more (e.g., about 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29 or more) nucleotides, wherein each strand comprises at least about 18 nucleotides that are complementary to the nucleotides of the other strand. In one embodiment, the siNA molecule is assembled from two oligonucleotide fragments, wherein one fragment comprises the nucleotide sequence of the antisense strand of the siNA molecule and a second fragment comprises nucleotide sequence of the sense region of the siNA molecule. In one embodiment, the sense strand is connected to the antisense strand via a linker molecule, such as a polynucleotide linker or a non-nucleotide linker. In a further embodiment, the pyrimidine nucleotides present in the sense strand are 2′-deoxy-2′fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-deoxy purine nucleotides. In another embodiment, the pyrimidine nucleotides present in the sense strand are 2′-deoxy-2′fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-O-methyl purine nucleotides. In still another embodiment, the pyrimidine nucleotides present in the antisense strand are 2′-deoxy-2′-fluoro pyrimidine nucleotides and any purine nucleotides present in the antisense strand are 2′-deoxy purine nucleotides. In another embodiment, the antisense strand comprises one or more 2′-deoxy-2′-fluoro pyrimidine nucleotides and one or more 2′-O-methyl purine nucleotides. In another embodiment, the pyrimidine nucleotides present in the antisense strand are 2′-deoxy-2′-fluoro pyrimidine nucleotides and any purine nucleotides present in the antisense strand are 2′-O-methyl purine nucleotides. In a further embodiment the sense strand comprises a 3′-end and a 5′-end, wherein a terminal cap moiety (e.g., an inverted deoxy abasic moiety or inverted deoxy nucleotide moiety such as inverted thymidine) is present at the 5′-end, the 3′-end, or both of the 5′ and 3′ ends of the sense strand. In another embodiment, the antisense strand comprises a phosphorothioate internucleotide linkage at the 3′ end of the antisense strand. In another embodiment, the antisense strand comprises a glyceryl modification at the 3′ end. In another embodiment, the 5′-end of the antisense strand optionally includes a phosphate group.

In any of the above-described embodiments of a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a BACE gene, wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification, each of the two strands of the siNA molecule can comprise about 21 nucleotides. In one embodiment, about 21 nucleotides of each strand of the siNA molecule are base-paired to the complementary nucleotides of the other strand of the siNA molecule. In another embodiment, about 19 nucleotides of each strand of the siNA molecule are base-paired to the complementary nucleotides of the other strand of the siNA molecule, wherein at least two 3′ terminal nucleotides of each strand of the siNA molecule are not base-paired to the nucleotides of the other strand of the siNA molecule. In another embodiment, each of the two 3′ terminal nucleotides of each fragment of the siNA molecule is a 2′-deoxy-pyrimidine, such as 2′-deoxy-thymidine. In one embodiment, each strand of the siNA molecule is base-paired to the complementary nucleotides of the other strand of the siNA molecule. In one embodiment, about 19 nucleotides of the antisense strand are base-paired to the nucleotide sequence of the BACE RNA or a portion thereof. In one embodiment, about 21 nucleotides of the antisense strand are base-paired to the nucleotide sequence of the BACE RNA or a portion thereof.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a BACE gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of BACE RNA or a portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification, and wherein the 5′-end of the antisense strand optionally includes a phosphate group.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a BACE gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of BACE RNA or a portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification, and wherein the nucleotide sequence or a portion thereof of the antisense strand is complementary to a nucleotide sequence of the untranslated region or a portion thereof of the BACE RNA.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a BACE gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of BACE RNA or a portion thereof, wherein the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand, wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification, and wherein the nucleotide sequence of the antisense strand is complementary to a nucleotide sequence of the BACE RNA or a portion thereof that is present in the BACE RNA.

In one embodiment, the invention features a composition comprising a siNA molecule of the invention in a pharmaceutically acceptable carrier or diluent.

In a non-limiting example, the introduction of chemically-modified nucleotides into nucleic acid molecules provides a powerful tool in overcoming potential limitations of in vivo stability and bioavailability inherent to native RNA molecules that are delivered exogenously. For example, the use of chemically-modified nucleic acid molecules can enable a lower dose of a particular nucleic acid molecule for a given therapeutic effect since chemically-modified nucleic acid molecules tend to have a longer half-life in serum. Furthermore, certain chemical modifications can improve the bioavailability of nucleic acid molecules by targeting particular cells or tissues and/or improving cellular uptake of the nucleic acid molecule. Therefore, even if the activity of a chemically-modified nucleic acid molecule is reduced as compared to a native nucleic acid molecule, for example, when compared to an all-RNA nucleic acid molecule, the overall activity of the modified nucleic acid molecule can be greater than that of the native molecule due to improved stability and/or delivery of the molecule. Unlike native unmodified siNA, chemically-modified siNA can also minimize the possibility of activating interferon activity in humans.

In any of the embodiments of siNA molecules described herein, the antisense region of a siNA molecule of the invention can comprise a phosphorothioate internucleotide linkage at the 3′-end of said antisense region. In any of the embodiments of siNA molecules described herein, the antisense region can comprise about one to about five phosphorothioate internucleotide linkages at the 5′-end of said antisense region. In any of the embodiments of siNA molecules described herein, the 3′-terminal nucleotide overhangs of a siNA molecule of the invention can comprise ribonucleotides or deoxyribonucleotides that are chemically-modified at a nucleic acid sugar, base, or backbone. In any of the embodiments of siNA molecules described herein, the 3′-terminal nucleotide overhangs can comprise one or more universal base ribonucleotides. In any of the embodiments of siNA molecules described herein, the 3′-terminal nucleotide overhangs can comprise one or more acyclic nucleotides.

One embodiment of the invention provides an expression vector comprising a nucleic acid sequence encoding at least one siNA molecule of the invention in a manner that allows expression of the nucleic acid molecule. Another embodiment of the invention provides a mammalian cell comprising such an expression vector. The mammalian cell can be a human cell. The siNA molecule of the expression vector can comprise a sense region and an antisense region. The antisense region can comprise sequence complementary to a RNA or DNA sequence encoding BACE and the sense region can comprise sequence complementary to the antisense region. The siNA molecule can comprise two distinct strands having complementary sense and antisense regions. The siNA molecule can comprise a single strand having complementary sense and antisense regions.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against BACE inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) nucleotides comprising a backbone modified internucleotide linkage having Formula I:

wherein each R1 and R2 is independently any nucleotide, non-nucleotide, or polynucleotide which can be naturally-occurring or chemically-modified, each X and Y is independently O, S, N, alkyl, or substituted alkyl, each Z and W is independently O, S, N, alkyl, substituted alkyl, O-alkyl, S-alkyl, alkaryl, aralkyl, or acetyl and wherein W, X, Y, and Z are optionally not all O. In another embodiment, a backbone modification of the invention comprises a phosphonoacetate and/or thiophosphonoacetate internucleotide linkage (see for example Sheehan et al., 2003, Nucleic Acids Research, 31, 4109-4118).

The chemically-modified internucleotide linkages having Formula I, for example, wherein any Z, W, X, and/or Y independently comprises a sulphur atom, can be present in one or both oligonucleotide strands of the siNA duplex, for example, in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) chemically-modified internucleotide linkages having Formula I at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified internucleotide linkages having Formula I at the 5′-end of the sense strand, the antisense strand, or both strands. In another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) pyrimidine nucleotides with chemically-modified internucleotide linkages having Formula I in the sense strand, the antisense strand, or both strands. In yet another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) purine nucleotides with chemically-modified internucleotide linkages having Formula I in the sense strand, the antisense strand, or both strands. In another embodiment, a siNA molecule of the invention having internucleotide linkage(s) of Formula I also comprises a chemically-modified nucleotide or non-nucleotide having any of Formulae I-VII.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against BACE inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) nucleotides or non-nucleotides having Formula II:

wherein each R3, R4, R5, R6, R7, R8, R10, R11 and R12 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OSH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-S-alkyl, alkyl-O-alkyl, ONO₂, NO₂, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I or II; R9 is O, S, CH2, S═O, CHF, or CF2, and B is a nucleosidic base such as adenine, guanine, uracil, cytosine, thymine, 2-aminoadenosine, 5-methylcytosine, 2,6-diaminopurine, or any other non-naturally occurring base that can be complementary or non-complementary to target RNA or a non-nucleosidic base such as phenyl, naphthyl, 3-nitropyrrole, 5-nitroindole, nebularine, pyridone, pyridinone, or any other non-naturally occurring universal base that can be complementary or non-complementary to target RNA.

The chemically-modified nucleotide or non-nucleotide of Formula II can be present in one or both oligonucleotide strands of the siNA duplex, for example in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more chemically-modified nucleotide or non-nucleotide of Formula II at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotides or non-nucleotides of Formula II at the 5′-end of the sense strand, the antisense strand, or both strands. In anther non-limiting example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotides or non-nucleotides of Formula II at the 3′-end of the sense strand, the antisense strand, or both strands.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against BACE inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) nucleotides or non-nucleotides having Formula III:

wherein each R3, R4, R5, R6, R7, R8, R10, R11 and R12 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OSH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-S-alkyl, alkyl-O-alkyl, ONO₂, NO₂, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I or II; R9 is O, S, CH2, S═O, CHF, or CF2, and B is a nucleosidic base such as adenine, guanine, uracil, cytosine, thymine, 2-aminoadenosine, 5-methylcytosine, 2,6-diaminopurine, or any other non-naturally occurring base that can be employed to be complementary or non-complementary to target RNA or a non-nucleosidic base such as phenyl, naphthyl, 3-nitropyrrole, 5-nitroindole, nebularine, pyridone, pyridinone, or any other non-naturally occurring universal base that can be complementary or non-complementary to target RNA.

The chemically-modified nucleotide or non-nucleotide of Formula III can be present in one or both oligonucleotide strands of the siNA duplex, for example, in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more chemically-modified nucleotide or non-nucleotide of Formula III at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotide(s) or non-nucleotide(s) of Formula III at the 5′-end of the sense strand, the antisense strand, or both strands. In anther non-limiting example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotide or non-nucleotide of Formula III at the 3′-end of the sense strand, the antisense strand, or both strands.

In another embodiment, a siNA molecule of the invention comprises a nucleotide having Formula II or III, wherein the nucleotide having Formula II or III is in an inverted configuration. For example, the nucleotide having Formula II or II is connected to the siNA construct in a 3′-3′,3′-2′,2′-3′, or 5′-5′ configuration, such as at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of one or both siNA strands.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against BACE inside a cell or reconstituted in vitro system, wherein the chemical modification comprises a 5′-terminal phosphate group having Formula IV:

wherein each X and Y is independently O, S, N, alkyl, substituted alkyl, or alkylhalo; wherein each Z and W is independently O, S, N, alkyl, substituted alkyl, O-alkyl, S-alkyl, alkaryl, aralkyl, alkylhalo, or acetyl; and wherein W, X, Y and Z are not all O.

In one embodiment, the invention features a siNA molecule having a 5′-terminal phosphate group having Formula IV on the target-complementary strand, for example, a strand complementary to a target RNA, wherein the siNA molecule comprises an all RNA siNA molecule. In another embodiment, the invention features a siNA molecule having a 5′-terminal phosphate group having Formula IV on the target-complementary strand wherein the siNA molecule also comprises about 1 to about 3 (e.g., about 1, 2, or 3) nucleotide 3′-terminal nucleotide overhangs having about 1 to about 4 (e.g., about 1, 2, 3, or 4) deoxyribonucleotides on the 3′-end of one or both strands. In another embodiment, a 5′-terminal phosphate group having Formula IV is present on the target-complementary strand of a siNA molecule of the invention, for example a siNA molecule having chemical modifications having any of Formulae I-VII.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against BACE inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more phosphorothioate internucleotide linkages. For example, in a non-limiting example, the invention features a chemically-modified short interfering nucleic acid (siNA) having about 1, 2, 3, 4, 5, 6, 7, 8 or more phosphorothioate internucleotide linkages in one siNA strand. In yet another embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) individually having about 1, 2, 3, 4, 5, 6, 7, 8 or more phosphorothioate internucleotide linkages in both siNA strands. The phosphorothioate internucleotide linkages can be present in one or both oligonucleotide strands of the siNA duplex, for example in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more phosphorothioate internucleotide linkages at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) consecutive phosphorothioate internucleotide linkages at the 5′-end of the sense strand, the antisense strand, or both strands. In another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) pyrimidine phosphorothioate internucleotide linkages in the sense strand, the antisense strand, or both strands. In yet another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) purine phosphorothioate internucleotide linkages in the sense strand, the antisense strand, or both strands.

In one embodiment, the invention features a siNA molecule, wherein the sense strand comprises one or more, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or about one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 10 or more, specifically about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2′-deoxy, 2′-O-methyl and/or 2′-deoxy-2′-fluoro nucleotides, with or without one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends, being present in the same or different strand.

In another embodiment, the invention features a siNA molecule, wherein the sense strand comprises about 1 to about 5, specifically about 1, 2, 3, 4, or 5 phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3-end, the 5′-end, or both of the 3′- and 5′-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 5 or more, specifically about 1, 2, 3, 4, 5, or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2′-deoxy, 2′-O-methyl and/or 2′-deoxy-2′-fluoro nucleotides, with or without about 1 to about 5 or more, for example about 1, 2, 3, 4, 5, or more phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends, being present in the same or different strand.

In one embodiment, the invention features a siNA molecule, wherein the antisense strand comprises one or more, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more phosphorothioate internucleotide linkages, and/or about one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 10 or more, specifically about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2′-deoxy, 2′-O-methyl and/or 2′-deoxy-2′-fluoro nucleotides, with or without one or more, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends, being present in the same or different strand.

In another embodiment, the invention features a siNA molecule, wherein the antisense strand comprises about 1 to about 5 or more, specifically about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 5 or more, specifically about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2′-deoxy, 2′-O-methyl and/or 2′-deoxy-2′-fluoro nucleotides, with or without about 1 to about 5, for example about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends, being present in the same or different strand.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule having about 1 to about 5 or more (specifically about 1, 2, 3, 4, 5 or more) phosphorothioate internucleotide linkages in each strand of the siNA molecule.

In another embodiment, the invention features a siNA molecule comprising 2′-5′ internucleotide linkages. The 2′-5′ internucleotide linkage(s) can be at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of one or both siNA sequence strands. In addition, the 2′-5′ internucleotide linkage(s) can be present at various other positions within one or both siNA sequence strands, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more including every internucleotide linkage of a pyrimidine nucleotide in one or both strands of the siNA molecule can comprise a 2′-5′ internucleotide linkage, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more including every internucleotide linkage of a purine nucleotide in one or both strands of the siNA molecule can comprise a 2′-5′ internucleotide linkage.

In another embodiment, a chemically-modified siNA molecule of the invention comprises a duplex having two strands, one or both of which can be chemically-modified, wherein each strand is about 18 to about 27 (e.g., about 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27) nucleotides in length, wherein the duplex has about 18 to about 23 (e.g., about 18, 19, 20, 21, 22, or 23) base pairs, and wherein the chemical modification comprises a structure having any of Formulae I-VII. For example, an exemplary chemically-modified siNA molecule of the invention comprises a duplex having two strands, one or both of which can be chemically-modified with a chemical modification having any of Formulae I-VII or any combination thereof, wherein each strand consists of about 21 nucleotides, each having a 2-nucleotide 3′-terminal nucleotide overhang, and wherein the duplex has about 19 base pairs. In another embodiment, a siNA molecule of the invention comprises a single stranded hairpin structure, wherein the siNA is about 36 to about 70 (e.g., about 36, 40, 45, 50, 55, 60, 65, or 70) nucleotides in length having about 18 to about 23 (e.g., about 18, 19, 20, 21, 22, or 23) base pairs, and wherein the siNA can include a chemical modification comprising a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises a linear oligonucleotide having about 42 to about 50 (e.g., about 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotides that is chemically-modified with a chemical modification having any of Formulae I-VII or any combination thereof, wherein the linear oligonucleotide forms a hairpin structure having about 19 base pairs and a 2-nucleotide 3′-terminal nucleotide overhang. In another embodiment, a linear hairpin siNA molecule of the invention contains a stem loop motif, wherein the loop portion of the siNA molecule is biodegradable. For example, a linear hairpin siNA molecule of the invention is designed such that degradation of the loop portion of the siNA molecule in vivo can generate a double-stranded siNA molecule with 3′-terminal overhangs, such as 3′-terminal nucleotide overhangs comprising about 2 nucleotides.

In another embodiment, a siNA molecule of the invention comprises a hairpin structure, wherein the siNA is about 25 to about 50 (e.g., about 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotides in length having about 3 to about 25 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) base pairs, and wherein the siNA can include one or more chemical modifications comprising a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises a linear oligonucleotide having about 25 to about 35 (e.g., about 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35) nucleotides that is chemically-modified with one or more chemical modifications having any of Formulae I-VII or any combination thereof, wherein the linear oligonucleotide forms a hairpin structure having about 3 to about 23 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23) base pairs and a 5′-terminal phosphate group that can be chemically modified as described herein (for example a 5′-terminal phosphate group having Formula IV). In another embodiment, a linear hairpin siNA molecule of the invention contains a stem loop motif, wherein the loop portion of the siNA molecule is biodegradable. In one embodiment, a linear hairpin siNA molecule of the invention comprises a loop portion comprising a non-nucleotide linker.

In another embodiment, a siNA molecule of the invention comprises an asymmetric hairpin structure, wherein the siNA is about 25 to about 50 (e.g., about 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotides in length having about 3 to about 20 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) base pairs, and wherein the siNA can include one or more chemical modifications comprising a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises a linear oligonucleotide having about 25 to about 35 (e.g., about 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35) nucleotides that is chemically-modified with one or more chemical modifications having any of Formulae I-VII or any combination thereof, wherein the linear oligonucleotide forms an asymmetric hairpin structure having about 3 to about 18 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18) base pairs and a 5′-terminal phosphate group that can be chemically modified as described herein (for example a 5′-terminal phosphate group having Formula IV). In one embodiment, an asymmetric hairpin siNA molecule of the invention contains a stem loop motif, wherein the loop portion of the siNA molecule is biodegradable. In another embodiment, an asymmetric hairpin siNA molecule of the invention comprises a loop portion comprising a non-nucleotide linker.

In another embodiment, a siNA molecule of the invention comprises an asymmetric double stranded structure having separate polynucleotide strands comprising sense and antisense regions, wherein the antisense region is about 16 to about 25 (e.g., about 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) nucleotides in length, wherein the sense region is about 3 to about 18 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18) nucleotides in length, wherein the sense region and the antisense region have at least 3 complementary nucleotides, and wherein the siNA can include one or more chemical modifications comprising a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises an asymmetric double stranded structure having separate polynucleotide strands comprising sense and antisense regions, wherein the antisense region is about 18 to about 22 (e.g., about 18, 19, 20, 21, or 22) nucleotides in length and wherein the sense region is about 3 to about 15 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15) nucleotides in length, wherein the sense region the antisense region have at least 3 complementary nucleotides, and wherein the siNA can include one or more chemical modifications comprising a structure having any of Formulae I-VII or any combination thereof. In another embodiment, the asymmetic double stranded siNA molecule can also have a 5′-terminal phosphate group that can be chemically modified as described herein (for example a 5′-terminal phosphate group having Formula IV).

In another embodiment, a siNA molecule of the invention comprises a circular nucleic acid molecule, wherein the siNA is about 38 to about 70 (e.g., about 38, 40, 45, 50, 55, 60, 65, or 70) nucleotides in length having about 18 to about 23 (e.g., about 18, 19, 20, 21, 22, or 23) base pairs, and wherein the siNA can include a chemical modification, which comprises a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises a circular oligonucleotide having about 42 to about 50 (e.g., about 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotides that is chemically-modified with a chemical modification having any of Formulae I-VII or any combination thereof, wherein the circular oligonucleotide forms a dumbbell shaped structure having about 19 base pairs and 2 loops.

In another embodiment, a circular siNA molecule of the invention contains two loop motifs, wherein one or both loop portions of the siNA molecule is biodegradable. For example, a circular siNA molecule of the invention is designed such that degradation of the loop portions of the siNA molecule in vivo can generate a double-stranded siNA molecule with 3′-terminal overhangs, such as 3′-terminal nucleotide overhangs comprising about 2 nucleotides.

In one embodiment, a siNA molecule of the invention comprises at least one (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) abasic moiety, for example a compound having Formula V:

wherein each R3, R4, R5, R6, R7, R8, R10, R11, R12, and R13 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OSH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-S-alkyl, alkyl-O-alkyl, ONO₂, NO2, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I or II; R9 is O, S, CH2, S═O, CHF, or CF2.

In one embodiment, a siNA molecule of the invention comprises at least one (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) inverted abasic moiety, for example a compound having Formula VI:

wherein each R3, R4, R5, R6, R7, R8, R10, R11, R12, and R13 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OSH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-S-alkyl, alkyl-O-alkyl, ONO₂, NO₂, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I or II; R9 is O, S, CH2, S═O, CHF, or CF2, and either R2, R3, R8 or R13 serve as points of attachment to the siNA molecule of the invention.

In another embodiment, a siNA molecule of the invention comprises at least one (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) substituted polyalkyl moieties, for example a compound having Formula VII:

wherein each n is independently an integer from 1 to 12, each R1, R2 and R3 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OSH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-S-alkyl, alkyl-O-alkyl, ONO₂, NO₂, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or a group having Formula I, and R1, R2 or R3 serves as points of attachment to the siNA molecule of the invention.

In another embodiment, the invention features a compound having Formula VII, wherein R1 and R2 are hydroxyl (OH) groups, n=1, and R3 comprises 0 and is the point of attachment to the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of one or both strands of a double-stranded siNA molecule of the invention or to a single-stranded siNA molecule of the invention. This modification is referred to herein as “glyceryl” (for example modification 6 in FIG. 10).

In another embodiment, a chemically modified nucleoside or non-nucleoside (e.g. a moiety having any of Formula V, VI or VII) of the invention is at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of a siNA molecule of the invention. For example, chemically modified nucleoside or non-nucleoside (e.g., a moiety having Formula V, VI or VII) can be present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense strand, the sense strand, or both antisense and sense strands of the siNA molecule. In one embodiment, the chemically modified nucleoside or non-nucleoside (e.g., a moiety having Formula V, VI or VII) is present at the 5′-end and 3′-end of the sense strand and the 3′-end of the antisense strand of a double stranded siNA molecule of the invention. In one embodiment, the chemically modified nucleoside or non-nucleoside (e.g., a moiety having Formula V, VI or VII) is present at the terminal position of the 5′-end and 3′-end of the sense strand and the 3′-end of the antisense strand of a double stranded siNA molecule of the invention. In one embodiment, the chemically modified nucleoside or non-nucleoside (e.g., a moiety having Formula V, VI or VII) is present at the two terminal positions of the 5′-end and 3′-end of the sense strand and the 3′-end of the antisense strand of a double stranded siNA molecule of the invention. In one embodiment, the chemically modified nucleoside or non-nucleoside (e.g., a moiety having Formula V, VI or VII) is present at the penultimate position of the 5′-end and 3′-end of the sense strand and the 3′-end of the antisense strand of a double stranded siNA molecule of the invention. In addition, a moiety having Formula VII can be present at the 3′-end or the 5′-end of a hairpin siNA molecule as described herein.

In another embodiment, a siNA molecule of the invention comprises an abasic residue having Formula V or VI, wherein the abasic residue having Formula VI or VI is connected to the siNA construct in a 3′-3′,3′-2′,2′-3′, or 5′-5′ configuration, such as at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of one or both siNA strands.

In one embodiment, a siNA molecule of the invention comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) locked nucleic acid (LNA) nucleotides, for example, at the 5′-end, the 3′-end, both of the 5′ and 3′-ends, or any combination thereof, of the siNA molecule.

In another embodiment, a siNA molecule of the invention comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) acyclic nucleotides, for example, at the 5′-end, the 3′-end, both of the 5′ and 3′-ends, or any combination thereof, of the siNA molecule.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising a sense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the sense region are 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides).

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising a sense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the sense region are 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides), wherein any nucleotides comprising a 3′-terminal nucleotide overhang that are present in said sense region are 2′-deoxy nucleotides.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising a sense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the sense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides).

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising a sense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), wherein any (e.g., one or more or all) purine nucleotides present in the sense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), and wherein any nucleotides comprising a 3′-terminal nucleotide overhang that are present in said sense region are 2′-deoxy nucleotides.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising an antisense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides).

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising an antisense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), and wherein any nucleotides comprising a 3′-terminal nucleotide overhang that are present in said antisense region are 2′-deoxy nucleotides.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising an antisense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides).

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising an antisense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides).

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention capable of mediating RNA interference (RNAi) against BACE inside a cell or reconstituted in vitro system comprising a sense region, wherein one or more pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and one or more purine nucleotides present in the sense region are 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides), and an antisense region, wherein one or more pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and one or more purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides). The sense region and/or the antisense region can have a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense and/or antisense sequence. The sense and/or antisense region can optionally further comprise a 3′-terminal nucleotide overhang having about 1 to about 4 (e.g., about 1, 2, 3, or 4) 2′-deoxynucleotides. The overhang nucleotides can further comprise one or more (e.g., about 1, 2, 3, 4 or more) phosphorothioate, phosphonoacetate, and/or thiophosphonoacetate internucleotide linkages. Non-limiting examples of these chemically-modified siNAs are shown in FIGS. 4 and 5 and Tables m and IV herein. In any of these described embodiments, the purine nucleotides present in the sense region are alternatively 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides) and one or more purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides). Also, in any of these embodiments, one or more purine nucleotides present in the sense region are alternatively purine ribonucleotides (e.g., wherein all purine nucleotides are purine ribonucleotides or alternately a plurality of purine nucleotides are purine ribonucleotides) and any purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides). Additionally, in any of these embodiments, one or more purine nucleotides present in the sense region and/or present in the antisense region are alternatively selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides (e.g., wherein all purine nucleotides are selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides or alternately a plurality of purine nucleotides are selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides).

In another embodiment, any modified nucleotides present in the siNA molecules of the invention, preferably in the antisense strand of the siNA molecules of the invention, but also optionally in the sense and/or both antisense and sense strands, comprise modified nucleotides having properties or characteristics similar to naturally occurring ribonucleotides. For example, the invention features siNA molecules including modified nucleotides having a Northern conformation (e.g., Northern pseudorotation cycle, see for example Saenger, Principles of Nucleic Acid Structure, Springer-Verlag ed., 1984). As such, chemically modified nucleotides present in the siNA molecules of the invention, preferably in the antisense strand of the siNA molecules of the invention, but also optionally in the sense and/or both antisense and sense strands, are resistant to nuclease degradation while at the same time maintaining the capacity to mediate RNAi. Non-limiting examples of nucleotides having a northern configuration include locked nucleic acid (LNA) nucleotides (e.g., 2′-O, 4′-C-methylene-(D-ribofuranosyl) nucleotides); 2′-methoxyethoxy(MOE) nucleotides; 2′-methyl-thio-ethyl, 2′-deoxy-2′-fluoro nucleotides, 2′-deoxy-2′-chloro nucleotides, 2′-azido nucleotides, and 2′-O-methyl nucleotides.

In one embodiment, the sense strand of a double stranded siNA molecule of the invention comprises a terminal cap moiety, (see for example FIG. 10) such as an inverted deoxyabaisc moiety, at the 3′-end, 5′-end, or both 3′ and 5′-ends of the sense strand.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid molecule (siNA) capable of mediating RNA interference (RNAi) against BACE inside a cell or reconstituted in vitro system, wherein the chemical modification comprises a conjugate covalently attached to the chemically-modified siNA molecule. Non-limiting examples of conjugates contemplated by the invention include conjugates and ligands described in Vargeese et al., U.S. Ser. No. 10/427,160, filed Apr. 30, 2003, incorporated by reference herein in its entirety, including the drawings. In another embodiment, the conjugate is covalently attached to the chemically-modified siNA molecule via a biodegradable linker. In one embodiment, the conjugate molecule is attached at the 3′-end of either the sense strand, the antisense strand, or both strands of the chemically-modified siNA molecule. In another embodiment, the conjugate molecule is attached at the 5′-end of either the sense strand, the antisense strand, or both strands of the chemically-modified siNA molecule. In yet another embodiment, the conjugate molecule is attached both the 3′-end and 5′-end of either the sense strand, the antisense strand, or both strands of the chemically-modified siNA molecule, or any combination thereof. In one embodiment, a conjugate molecule of the invention comprises a molecule that facilitates delivery of a chemically-modified siNA molecule into a biological system, such as a cell. In another embodiment, the conjugate molecule attached to the chemically-modified siNA molecule is a polyethylene glycol, human serum albumin, or a ligand for a cellular receptor that can mediate cellular uptake. Examples of specific conjugate molecules contemplated by the instant invention that can be attached to chemically-modified siNA molecules are described in Vargeese et al., U.S. Ser. No. 10/201,394, filed Jul. 22, 2002 incorporated by reference herein. The type of conjugates used and the extent of conjugation of siNA molecules of the invention can be evaluated for improved pharmacokinetic profiles, bioavailability, and/or stability of siNA constructs while at the same time maintaining the ability of the siNA to mediate RNAi activity. As such, one skilled in the art can screen siNA constructs that are modified with various conjugates to determine whether the siNA conjugate complex possesses improved properties while maintaining the ability to mediate RNAi, for example in animal models as are generally known in the art.

In one embodiment, the invention features a short interfering nucleic acid (siNA) molecule of the invention, wherein the siNA further comprises a nucleotide, non-nucleotide, or mixed nucleotide/non-nucleotide linker that joins the sense region of the siNA to the antisense region of the siNA. In one embodiment, a nucleotide linker of the invention can be a linker of >2 nucleotides in length, for example about 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides in length. In another embodiment, the nucleotide linker can be a nucleic acid aptamer. By “aptamer” or “nucleic acid aptamer” as used herein is meant a nucleic acid molecule that binds specifically to a target molecule wherein the nucleic acid molecule has sequence that comprises a sequence recognized by the target molecule in its natural setting. Alternately, an aptamer can be a nucleic acid molecule that binds to a target molecule where the target molecule does not naturally bind to a nucleic acid. The target molecule can be any molecule of interest. For example, the aptamer can be used to bind to a ligand-binding domain of a protein, thereby preventing interaction of the naturally occurring ligand with the protein. This is a non-limiting example and those in the art will recognize that other embodiments can be readily generated using techniques generally known in the art. (See, for example, Gold et al., 1995, Annu. Rev. Biochem., 64, 763; Brody and Gold, 2000, J. Biotechnol., 74, 5; Sun, 2000, Curr. Opin. Mol. Ther., 2, 100; Kusser, 2000, J. Biotechnol., 74, 27; Hermann and Patel, 2000, Science, 287, 820; and Jayasena, 1999, Clinical Chemistry, 45, 1628.)

In yet another embodiment, a non-nucleotide linker of the invention comprises abasic nucleotide, polyether, polyamine, polyamide, peptide, carbohydrate, lipid, polyhydrocarbon, or other polymeric compounds (e.g. polyethylene glycols such as those having between 2 and 100 ethylene glycol units). Specific examples include those described by Seela and Kaiser, Nucleic Acids Res. 1990, 18:6353 and Nucleic Acids Res. 1987, 15:3113; Cload and Schepartz, J. Am. Chem. Soc. 1991, 113:6324; Richardson and Schepartz, J. Am. Chem. Soc. 1991, 113:5109; Ma et al., Nucleic Acids Res. 1993, 21:2585 and Biochemistry 1993, 32:1751; Durand et al., Nucleic Acids Res. 1990, 18:6353; McCurdy et al., Nucleosides & Nucleotides 1991, 10:287; Jschke et al., Tetrahedron Lett. 1993, 34:301; Ono et al., Biochemistry 1991, 30:9914; Arnold et al., International Publication No. WO 89/02439; Usman et al., International Publication No. WO 95/06731; Dudycz et al., International Publication No. WO 95/11910 and Ferentz and Verdine, J. Am. Chem. Soc. 1991, 113:4000, all hereby incorporated by reference herein. A “non-nucleotide” further means any group or compound that can be incorporated into a nucleic acid chain in the place of one or more nucleotide units, including either sugar and/or phosphate substitutions, and allows the remaining bases to exhibit their enzymatic activity. The group or compound can be abasic in that it does not contain a commonly recognized nucleotide base, such as adenosine, guanine, cytosine, uracil or thymine, for example at the C1 position of the sugar.

In one embodiment, the invention features a short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) inside a cell or reconstituted in vitro system, wherein one or both strands of the siNA molecule that are assembled from two separate oligonucleotides do not comprise any ribonucleotides. For example, a siNA molecule can be assembled from a single oligonculeotide where the sense and antisense regions of the siNA comprise separate oligonucleotides that do not have any ribonucleotides (e.g., nucleotides having a 2′-OH group) present in the oligonucleotides. In another example, a siNA molecule can be assembled from a single oligonculeotide where the sense and antisense regions of the siNA are linked or circularized by a nucleotide or non-nucleotide linker as described herein, wherein the oligonucleotide does not have any ribonucleotides (e.g., nucleotides having a 2′-OH group) present in the oligonucleotide. Applicant has surprisingly found that the presense of ribonucleotides (e.g., nucleotides having a 2′-hydroxyl group) within the siNA molecule is not required or essential to support RNAi activity. As such, in one embodiment, all positions within the siNA can include chemically modified nucleotides and/or non-nucleotides such as nucleotides and or non-nucleotides having Formula I, II, III, IV, V, VI, or VII or any combination thereof to the extent that the ability of the siNA molecule to support RNAi activity in a cell is maintained.

In one embodiment, a siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system comprising a single stranded polynucleotide having complementarity to a target nucleic acid sequence. In another embodiment, the single stranded siNA molecule of the invention comprises a 5′-terminal phosphate group. In another embodiment, the single stranded siNA molecule of the invention comprises a 5′-terminal phosphate group and a 3′-terminal phosphate group (e.g., a 2′,3′-cyclic phosphate). In another embodiment, the single stranded siNA molecule of the invention comprises about 18 to about 29 (e.g., about 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29) nucleotides. In yet another embodiment, the single stranded siNA molecule of the invention comprises one or more chemically modified nucleotides or non-nucleotides described herein. For example, all the positions within the siNA molecule can include chemically-modified nucleotides such as nucleotides having any of Formulae I-VII, or any combination thereof to the extent that the ability of the siNA molecule to support RNAi activity in a cell is maintained.

In one embodiment, a siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system comprising a single stranded polynucleotide having complementarity to a target nucleic acid sequence, wherein one or more pyrimidine nucleotides present in the siNA are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), and a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense sequence. The sNA optionally further comprises about 1 to about 4 or more (e.g., about 1, 2, 3, 4 or more) terminal 2′-deoxynucleotides at the 3′-end of the siNA molecule, wherein the terminal nucleotides can further comprise one or more (e.g., 1, 2, 3, 4 or more) phosphorothioate, phosphonoacetate, and/or thiophosphonoacetate internucleotide linkages, and wherein the siNA optionally further comprises a terminal phosphate group, such as a 5′-terminal phosphate group. In any of these embodiments, any purine nucleotides present in the antisense region are alternatively 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides). Also, in any of these embodiments, any purine nucleotides present in the siNA (i.e., purine nucleotides present in the sense and/or antisense region) can alternatively be locked nucleic acid (LNA) nucleotides (e.g., wherein all purine nucleotides are LNA nucleotides or alternately a plurality of purine nucleotides are LNA nucleotides). Also, in any of these embodiments, any purine nucleotides present in the siNA are alternatively 2′-methoxyethyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-methoxyethyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-methoxyethyl purine nucleotides). In another embodiment, any modified nucleotides present in the single stranded siNA molecules of the invention comprise modified nucleotides having properties or characteristics similar to naturally occurring ribonucleotides. For example, the invention features siNA molecules including modified nucleotides having a Northern conformation (e.g., Northern pseudorotation cycle, see for example Saenger, Principles of Nucleic Acid Structure, Springer-Verlag ed., 1984). As such, chemically modified nucleotides present in the single stranded siNA molecules of the invention are preferably resistant to nuclease degradation while at the same time maintaining the capacity to mediate RNAi.

In one embodiment, the invention features a method for modulating the expression of a BACE gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the BACE gene; and (b) introducing the siNA molecule into a cell under conditions suitable to modulate the expression of the BACE gene in the cell.

In one embodiment, the invention features a method for modulating the expression of a BACE gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the BACE gene and wherein the sense strand sequence of the siNA comprises a sequence identical or substantially similar to the sequence of the target RNA; and (b) introducing the siNA molecule into a cell under conditions suitable to modulate the expression of the BACE gene in the cell.

In another embodiment, the invention features a method for modulating the expression of more than one BACE gene within a cell comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the BACE genes; and (b) introducing the siNA molecules into a cell under conditions suitable to modulate the expression of the BACE genes in the cell.

In another embodiment, the invention features a method for modulating the expression of two or more BACE genes within a cell comprising: (a) synthesizing one or more siNA molecules of the invention, which can be chemically-modified, wherein the siNA strands comprise sequences complementary to RNA of the BACE genes and wherein the sense strand sequences of the siNAs comprise sequences identical or substantially similar to the sequences of the target RNAs; and (b) introducing the siNA molecules into a cell under conditions suitable to modulate the expression of the BACE genes in the cell.

In another embodiment, the invention features a method for modulating the expression of more than one BACE gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the BACE gene and wherein the sense strand sequence of the siNA comprises a sequence identical or substantially similar to the sequences of the target RNAs; and (b) introducing the siNA molecule into a cell under conditions suitable to modulate the expression of the BACE genes in the cell.

In one embodiment, siNA molecules of the invention are used as reagents in ex vivo applications. For example, siNA reagents are introduced into tissue or cells that are transplanted into a subject for therapeutic effect. The cells and/or tissue can be derived from an organism or subject that later receives the explant, or can be derived from another organism or subject prior to transplantation. The siNA molecules can be used to modulate the expression of one or more genes in the cells or tissue, such that the cells or tissue obtain a desired phenotype or are able to perform a function when transplanted in vivo. In one embodiment, certain target cells from a patient are extracted. These extracted cells are contacted with siNAs targeting a specific nucleotide sequence within the cells under conditions suitable for uptake of the siNAs by these cells (e.g. using delivery reagents such as cationic lipids, liposomes and the like or using techniques such as electroporation to facilitate the delivery of siNAs into cells). The cells are then reintroduced back into the same patient or other patients. In one embodiment, the invention features a method of modulating the expression of a BACE gene in a tissue explant comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the BACE gene; and (b) introducing the siNA molecule into a cell of the tissue explant derived from a particular organism under conditions suitable to modulate the expression of the BACE gene in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the organism the tissue was derived from or into another organism under conditions suitable to modulate the expression of the BACE gene in that organism.

In one embodiment, the invention features a method of modulating the expression of a BACE gene in a tissue explant comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the BACE gene and wherein the sense strand sequence of the siNA comprises a sequence identical or substantially similar to the sequence of the target RNA; and (b) introducing the siNA molecule into a cell of the tissue explant derived from a particular organism under conditions suitable to modulate the expression of the BACE gene in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the organism the tissue was derived from or into another organism under conditions suitable to modulate the expression of the BACE gene in that organism.

In another embodiment, the invention features a method of modulating the expression of more than one BACE gene in a tissue explant comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the BACE genes; and (b) introducing the siNA molecules into a cell of the tissue explant derived from a particular organism under conditions suitable to modulate the expression of the BACE genes in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the organism the tissue was derived from or into another organism under conditions suitable to modulate the expression of the BACE genes in that organism.

In one embodiment, the invention features a method of modulating the expression of a BACE gene in a subject or organism comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the BACE gene; and (b) introducing the siNA molecule into the subject or organism under conditions suitable to modulate the expression of the BACE gene in the subject or organism. The level of BACE protein or RNA can be determined using various methods well-known in the art.

In another embodiment, the invention features a method of modulating the expression of more than one BACE gene in a subject or organism comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the BACE genes; and (b) introducing the siNA molecules into the subject or organism under conditions suitable to modulate the expression of the BACE genes in the subject or organism. The level of BACE protein or RNA can be determined as is known in the art.

In one embodiment, the invention features a method for modulating the expression of a BACE gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the BACE gene; and (b) introducing the siNA molecule into a cell under conditions suitable to modulate the expression of the BACE gene in the cell.

In another embodiment, the invention features a method for modulating the expression of more than one BACE gene within a cell comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the BACE gene; and (b) contacting the cell in vitro or in vivo with the siNA molecule under conditions suitable to modulate the expression of the BACE genes in the cell.

In one embodiment, the invention features a method of modulating the expression of a BACE gene in a tissue explant comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the BACE gene; and (b) contacting a cell of the tissue explant derived from a particular subject or organism with the siNA molecule under conditions suitable to modulate the expression of the BACE gene in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the subject or organism the tissue was derived from or into another subject or organism under conditions suitable to modulate the expression of the BACE gene in that subject or organism.

In another embodiment, the invention features a method of modulating the expression of more than one BACE gene in a tissue explant comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the BACE gene; and (b) introducing the siNA molecules into a cell of the tissue explant derived from a particular subject or organism under conditions suitable to modulate the expression of the BACE genes in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the subject or organism the tissue was derived from or into another subject or organism under conditions suitable to modulate the expression of the BACE genes in that subject or organism.

In one embodiment, the invention features a method of modulating the expression of a BACE gene in a subject or organism comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the BACE gene; and (b) introducing the sNA molecule into the subject or organism under conditions suitable to modulate the expression of the BACE gene in the subject or organism.

In another embodiment, the invention features a method of modulating the expression of more than one BACE gene in a subject or organism comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the BACE gene; and (b) introducing the siNA molecules into the subject or organism under conditions suitable to modulate the expression of the BACE genes in the subject or organism.

In one embodiment, the invention features a method of modulating the expression of a BACE gene in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the BACE gene in the subject or organism.

In one embodiment, the invention features a method for treating Alzheimer's disease in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the BACE gene in the subject or organism.

In one embodiment, the invention features a method for treating neurodegenerative disorders or conditions, such as dementia, in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the BACE gene in the subject or organism.

In one embodiment, the invention features a method for treating stroke/cardiovascular accident in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the BACE gene in the subject or organism.

In another embodiment, the invention features a method of modulating the expression of more than one BACE gene in a subject or organism comprising contacting the subject or organism with one or more siNA molecules of the invention under conditions suitable to modulate the expression of the BACE genes in the subject or organism.

The siNA molecules of the invention can be designed to down regulate or inhibit target (e.g., BACE) gene expression through RNAi targeting of a variety of RNA molecules. In one embodiment, the siNA molecules of the invention are used to target various RNAs corresponding to a target gene. Non-limiting examples of such RNAs include messenger RNA (mRNA), alternate RNA splice variants of target gene(s), post-transcriptionally modified RNA of target gene(s), pre-mRNA of target gene(s), and/or RNA templates. If alternate splicing produces a family of transcripts that are distinguished by usage of appropriate exons, the instant invention can be used to inhibit gene expression through the appropriate exons to specifically inhibit or to distinguish among the functions of gene family members. For example, a protein that contains an alternatively spliced transmembrane domain can be expressed in both membrane bound and secreted forms. Use of the invention to target the exon containing the transmembrane domain can be used to determine the functional consequences of pharmaceutical targeting of membrane bound as opposed to the secreted form of the protein. Non-limiting examples of applications of the invention relating to targeting these RNA molecules include therapeutic pharmaceutical applications, pharmaceutical discovery applications, molecular diagnostic and gene function applications, and gene mapping, for example using single nucleotide polymorphism mapping with siNA molecules of the invention. Such applications can be implemented using known gene sequences or from partial sequences available from an expressed sequence tag (EST).

In another embodiment, the siNA molecules of the invention are used to target conserved sequences corresponding to a gene family or gene families such as BACE family genes. As such, siNA molecules targeting multiple BACE targets can provide increased therapeutic effect. In addition, siNA can be used to characterize pathways of gene function in a variety of applications. For example, the present invention can be used to inhibit the activity of target gene(s) in a pathway to determine the function of uncharacterized gene(s) in gene function analysis, mRNA function analysis, or translational analysis. The invention can be used to determine potential target gene pathways involved in various diseases and conditions toward pharmaceutical development. The invention can be used to understand pathways of gene expression involved in, for example, Alzheimer's disease and other neurodegenerative disorders or conditions, such as dementia, and stroke/cardiovascular accident.

In one embodiment, siNA molecule(s) and/or methods of the invention are used to down regulate the expression of gene(s) that encode RNA referred to by Genbank Accession, for example, BACE genes encoding RNA sequence(s) referred to herein by Genbank Accession number, for example, Genbank Accession Nos. shown in Table I.

In one embodiment, the invention features a method comprising: (a) generating a library of siNA constructs having a predetermined complexity; and (b) assaying the siNA constructs of (a) above, under conditions suitable to determine RNAi target sites within the target RNA sequence. In one embodiment, the siNA molecules of (a) have strands of a fixed length, for example, about 23 nucleotides in length. In another embodiment, the siNA molecules of (a) are of differing length, for example having strands of about 18 to about 25 (e.g., about 18, 19, 20, 21, 22, 23, 24, or 25) nucleotides in length. In one embodiment, the assay can comprise a reconstituted in vitro siNA assay as described herein. In another embodiment, the assay can comprise a cell culture system in which target RNA is expressed. In another embodiment, fragments of target RNA are analyzed for detectable levels of cleavage, for example by gel electrophoresis, northern blot analysis, or RNAse protection assays, to determine the most suitable target site(s) within the target RNA sequence. The target RNA sequence can be obtained as is known in the art, for example, by cloning and/or transcription for in vitro systems, and by cellular expression in in vivo systems.

In one embodiment, the invention features a method comprising: (a) generating a randomized library of siNA constructs having a predetermined complexity, such as of 4N, where N represents the number of base paired nucleotides in each of the sNA construct strands (e.g. for a siNA construct having 21 nucleotide sense and antisense strands with 19 base pairs, the complexity would be 419); and (b) assaying the siNA constructs of (a) above, under conditions suitable to determine RNAi target sites within the target BACE RNA sequence. In another embodiment, the sNA molecules of (a) have strands of a fixed length, for example about 23 nucleotides in length. In yet another embodiment, the siNA molecules of (a) are of differing length, for example having strands of about 18 to about 25 (e.g., about 18, 19, 20, 21, 22, 23, 24, or 25) nucleotides in length. In one embodiment, the assay can comprise a reconstituted in vitro siNA assay as described in Example 7 herein. In another embodiment, the assay can comprise a cell culture system in which target RNA is expressed. In another embodiment, fragments of BACE RNA are analyzed for detectable levels of cleavage, for example, by gel electrophoresis, northern blot analysis, or RNAse protection assays, to determine the most suitable target site(s) within the target BACE RNA sequence. The target BACE RNA sequence can be obtained as is known in the art, for example, by cloning and/or transcription for in vitro systems, and by cellular expression in in vivo systems.

In another embodiment, the invention features a method comprising: (a) analyzing the sequence of a RNA target encoded by a target gene; (b) synthesizing one or more sets of siNA molecules having sequence complementary to one or more regions of the RNA of (a); and (c) assaying the siNA molecules of (b) under conditions suitable to determine RNAi targets within the target RNA sequence. In one embodiment, the siNA molecules of (b) have strands of a fixed length, for example about 23 nucleotides in length. In another embodiment, the siNA molecules of (b) are of differing length, for example having strands of about 18 to about 25 (e.g., about 18, 19, 20, 21, 22, 23, 24, or 25) nucleotides in length. In one embodiment, the assay can comprise a reconstituted in vitro siNA assay as described herein. In another embodiment, the assay can comprise a cell culture system in which target RNA is expressed. Fragments of target RNA are analyzed for detectable levels of cleavage, for example by gel electrophoresis, northern blot analysis, or RNAse protection assays, to determine the most suitable target site(s) within the target RNA sequence. The target RNA sequence can be obtained as is known in the art, for example, by cloning and/or transcription for in vitro systems, and by expression in in vivo systems.

By “target site” is meant a sequence within a target RNA that is “targeted” for cleavage mediated by a sNA construct which contains sequences within its antisense region that are complementary to the target sequence.

By “detectable level of cleavage” is meant cleavage of target RNA (and formation of cleaved product RNAs) to an extent sufficient to discern cleavage products above the background of RNAs produced by random degradation of the target RNA. Production of cleavage products from 1-5% of the target RNA is sufficient to detect above the background for most methods of detection.

In one embodiment, the invention features a composition comprising a siNA molecule of the invention, which can be chemically-modified, in a pharmaceutically acceptable carrier or diluent. In another embodiment, the invention features a pharmaceutical composition comprising siNA molecules of the invention, which can be chemically-modified, targeting one or more genes in a pharmaceutically acceptable carrier or diluent. In another embodiment, the invention features a method for diagnosing a disease or condition in a subject comprising administering to the subject a composition of the invention under conditions suitable for the diagnosis of the disease or condition in the subject. In another embodiment, the invention features a method for treating or preventing a disease or condition in a subject, comprising administering to the subject a composition of the invention under conditions suitable for the treatment or prevention of the disease or condition in the subject, alone or in conjunction with one or more other therapeutic compounds. In yet another embodiment, the invention features a method for treating Alzheimer's disease and/or other neurodegenerative disorders, such as dementia and stroke/cardiovascular accident in a subject comprising administering to the subject a composition of the invention under conditions suitable for the treatment of Alzheimer's disease and/or other neurodegenerative disorders, such as dementia and stroke/cardiovascular accident in the subject.

In another embodiment, the invention features a method for validating a BACE gene target, comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands includes a sequence complementary to RNA of a BACE target gene; (b) introducing the siNA molecule into a cell, tissue, subject or organism under conditions suitable for modulating expression of the BACE target gene in the cell, tissue, subject, or organism; and (c) determining the function of the gene by assaying for any phenotypic change in the cell, tissue, subject, or organism.

In another embodiment, the invention features a method for validating a BACE target comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands includes a sequence complementary to RNA of a BACE target gene; (b) introducing the siNA molecule into a biological system under conditions suitable for modulating expression of the BACE target gene in the biological system; and (c) determining the function of the gene by assaying for any phenotypic change in the biological system.

By “biological system” is meant, material, in a purified or unpurified form, from biological sources, including but not limited to human or animal, wherein the system comprises the components required for RNAi activity. The term “biological system” includes, for example, a cell, tissue, subject, or organism, or extract thereof. The term biological system also includes reconstituted RNAi systems that can be used in an in vitro setting.

By “phenotypic change” is meant any detectable change to a cell that occurs in response to contact or treatment with a nucleic acid molecule of the invention (e.g., siNA). Such detectable changes include, but are not limited to, changes in shape, size, proliferation, motility, protein expression or RNA expression or other physical or chemical changes as can be assayed by methods known in the art. The detectable change can also include expression of reporter genes/molecules such as Green Florescent Protein (GFP) or various tags that are used to identify an expressed protein or any other cellular component that can be assayed.

In one embodiment, the invention features a kit containing a siNA molecule of the invention, which can be chemically-modified, that can be used to modulate the expression of a BACE target gene in a biological system, including, for example, in a cell, tissue, subject, or organism. In another embodiment, the invention features a kit containing more than one siNA molecule of the invention, which can be chemically-modified, that can be used to modulate the expression of more than one BACE target gene in a biological system, including, for example, in a cell, tissue, subject, or organism.

In one embodiment, the invention features a cell containing one or more siNA molecules of the invention, which can be chemically-modified. In another embodiment, the cell containing a siNA molecule of the invention is a mammalian cell. In yet another embodiment, the cell containing a siNA molecule of the invention is a human cell.

In one embodiment, the synthesis of a sNA molecule of the invention, which can be chemically-modified, comprises: (a) synthesis of two complementary strands of the siNA molecule; (b) annealing the two complementary strands together under conditions suitable to obtain a double-stranded siNA molecule. In another embodiment, synthesis of the two complementary strands of the siNA molecule is by solid phase oligonucleotide synthesis. In yet another embodiment, synthesis of the two complementary strands of the siNA molecule is by solid phase tandem oligonucleotide synthesis.

In one embodiment, the invention features a method for synthesizing a siNA duplex molecule comprising: (a) synthesizing a first oligonucleotide sequence strand of the siNA molecule, wherein the first oligonucleotide sequence strand comprises a cleavable linker molecule that can be used as a scaffold for the synthesis of the second oligonucleotide sequence strand of the siNA; (b) synthesizing the second oligonucleotide sequence strand of siNA on the scaffold of the first oligonucleotide sequence strand, wherein the second oligonucleotide sequence strand further comprises a chemical moiety than can be used to purify the siNA duplex; (c) cleaving the linker molecule of (a) under conditions suitable for the two siNA oligonucleotide strands to hybridize and form a stable duplex; and (d) purifying the siNA duplex utilizing the chemical moiety of the second oligonucleotide sequence strand. In one embodiment, cleavage of the linker molecule in (c) above takes place during deprotection of the oligonucleotide, for example, under hydrolysis conditions using an alkylamine base such as methylamine. In one embodiment, the method of synthesis comprises solid phase synthesis on a solid support such as controlled pore glass (CPG) or polystyrene, wherein the first sequence of (a) is synthesized on a cleavable linker, such as a succinyl linker, using the solid support as a scaffold. The cleavable linker in (a) used as a scaffold for synthesizing the second strand can comprise similar reactivity as the solid support derivatized linker, such that cleavage of the solid support derivatized linker and the cleavable linker of (a) takes place concomitantly. In another embodiment, the chemical moiety of (b) that can be used to isolate the attached oligonucleotide sequence comprises a trityl group, for example a dimethoxytrityl group, which can be employed in a trityl-on synthesis strategy as described herein. In yet another embodiment, the chemical moiety, such as a dimethoxytrityl group, is removed during purification, for example, using acidic conditions.

In a further embodiment, the method for siNA synthesis is a solution phase synthesis or hybrid phase synthesis wherein both strands of the siNA duplex are synthesized in tandem using a cleavable linker attached to the first sequence which acts a scaffold for synthesis of the second sequence. Cleavage of the linker under conditions suitable for hybridization of the separate siNA sequence strands results in formation of the double-stranded siNA molecule.

In another embodiment, the invention features a method for synthesizing a siNA duplex molecule comprising: (a) synthesizing one oligonucleotide sequence strand of the siNA molecule, wherein the sequence comprises a cleavable linker molecule that can be used as a scaffold for the synthesis of another oligonucleotide sequence; (b) synthesizing a second oligonucleotide sequence having complementarity to the first sequence strand on the scaffold of (a), wherein the second sequence comprises the other strand of the double-stranded siNA molecule and wherein the second sequence further comprises a chemical moiety than can be used to isolate the attached oligonucleotide sequence; (c) purifying the product of (b) utilizing the chemical moiety of the second oligonucleotide sequence strand under conditions suitable for isolating the full-length sequence comprising both siNA oligonucleotide strands connected by the cleavable linker and under conditions suitable for the two siNA oligonucleotide strands to hybridize and form a stable duplex. In one embodiment, cleavage of the linker molecule in (c) above takes place during deprotection of the oligonucleotide, for example, under hydrolysis conditions. In another embodiment, cleavage of the linker molecule in (c) above takes place after deprotection of the oligonucleotide. In another embodiment, the method of synthesis comprises solid phase synthesis on a solid support such as controlled pore glass (CPG) or polystyrene, wherein the first sequence of (a) is synthesized on a cleavable linker, such as a succinyl linker, using the solid support as a scaffold. The cleavable linker in (a) used as a scaffold for synthesizing the second strand can comprise similar reactivity or differing reactivity as the solid support derivatized linker, such that cleavage of the solid support derivatized linker and the cleavable linker of (a) takes place either concomitantly or sequentially. In one embodiment, the chemical moiety of (b) that can be used to isolate the attached oligonucleotide sequence comprises a trityl group, for example a dimethoxytrityl group.

In another embodiment, the invention features a method for making a double-stranded siNA molecule in a single synthetic process comprising: (a) synthesizing an oligonucleotide having a first and a second sequence, wherein the first sequence is complementary to the second sequence, and the first oligonucleotide sequence is linked to the second sequence via a cleavable linker, and wherein a terminal 5′-protecting group, for example, a 5′-O-dimethoxytrityl group (5′-O-DMT) remains on the oligonucleotide having the second sequence; (b) deprotecting the oligonucleotide whereby the deprotection results in the cleavage of the linker joining the two oligonucleotide sequences; and (c) purifying the product of (b) under conditions suitable for isolating the double-stranded siNA molecule, for example using a trityl-on synthesis strategy as described herein.

In another embodiment, the method of synthesis of siNA molecules of the invention comprises the teachings of Scaringe et al., U.S. Pat. Nos. 5,889,136; 6,008,400; and 6,111,086, incorporated by reference herein in their entirety.

In one embodiment, the invention features siNA constructs that mediate RNAi against BACE, wherein the siNA construct comprises one or more chemical modifications, for example, one or more chemical modifications having any of Formulae I-VII or any combination thereof that increases the nuclease resistance of the siNA construct.

In another embodiment, the invention features a method for generating siNA molecules with increased nuclease resistance comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased nuclease resistance.

In one embodiment, the invention features siNA constructs that mediate RNAi against BACE, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the binding affinity between the sense and antisense strands of the sNA construct.

In another embodiment, the invention features a method for generating siNA molecules with increased binding affinity between the sense and antisense strands of the siNA molecule comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased binding affinity between the sense and antisense strands of the siNA molecule.

In one embodiment, the invention features siNA constructs that mediate RNAi against BACE, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the binding affinity between the antisense strand of the siNA construct and a complementary target RNA sequence within a cell.

In one embodiment, the invention features siNA constructs that mediate RNAi against BACE, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the binding affinity between the antisense strand of the siNA construct and a complementary target DNA sequence within a cell.

In another embodiment, the invention features a method for generating siNA molecules with increased binding affinity between the antisense strand of the siNA molecule and a complementary target RNA sequence comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased binding affinity between the antisense strand of the siNA molecule and a complementary target RNA sequence.

In another embodiment, the invention features a method for generating siNA molecules with increased binding affinity between the antisense strand of the siNA molecule and a complementary target DNA sequence comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased binding affinity between the antisense strand of the siNA molecule and a complementary target DNA sequence.

In one embodiment, the invention features siNA constructs that mediate RNAi against BACE, wherein the siNA construct comprises one or more chemical modifications described herein that modulate the polymerase activity of a cellular polymerase capable of generating additional endogenous siNA molecules having sequence homology to the chemically-modified siNA construct.

In another embodiment, the invention features a method for generating siNA molecules capable of mediating increased polymerase activity of a cellular polymerase capable of generating additional endogenous siNA molecules having sequence homology to a chemically-modified siNA molecule comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules capable of mediating increased polymerase activity of a cellular polymerase capable of generating additional endogenous siNA molecules having sequence homology to the chemically-modified siNA molecule.

In one embodiment, the invention features chemically-modified siNA constructs that mediate RNAi against BACE in a cell, wherein the chemical modifications do not significantly effect the interaction of siNA with a target RNA molecule, DNA molecule and/or proteins or other factors that are essential for RNAi in a manner that would decrease the efficacy of RNAi mediated by such siNA constructs.

In another embodiment, the invention features a method for generating siNA molecules with improved RNAi activity against BACE comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved RNAi activity.

In yet another embodiment, the invention features a method for generating siNA molecules with improved RNAi activity against BACE target RNA comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved RNAi activity against the target RNA.

In yet another embodiment, the invention features a method for generating siNA molecules with improved RNAi activity against BACE target DNA comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved RNAi activity against the target DNA.

In one embodiment, the invention features siNA constructs that mediate RNAi against BACE, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the cellular uptake of the siNA construct.

In another embodiment, the invention features a method for generating siNA molecules against BACE with improved cellular uptake comprising (a) introducing nucleotides having any of Formula I-VI or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved cellular uptake.

In one embodiment, the invention features siNA constructs that mediate RNAi against BACE, wherein the siNA construct comprises one or more chemical modifications described herein that increases the bioavailability of the siNA construct, for example, by attaching polymeric conjugates such as polyethyleneglycol or equivalent conjugates that improve the pharmacokinetics of the siNA construct, or by attaching conjugates that target specific tissue types or cell types in vivo. Non-limiting examples of such conjugates are described in Vargeese et al., U.S. Ser. No. 10/201,394 incorporated by reference herein.

In one embodiment, the invention features a method for generating siNA molecules of the invention with improved bioavailability comprising (a) introducing a conjugate into the structure of a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved bioavailability. Such conjugates can include ligands for cellular receptors, such as peptides derived from naturally occurring protein ligands; protein localization sequences, including cellular ZIP code sequences; antibodies; nucleic acid aptamers; vitamins and other co-factors, such as folate and N-acetylgalactosamine; polymers, such as polyethyleneglycol (PEG); phospholipids; cholesterol; polyamines, such as spermine or spermidine; and others.

In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein said second sequence is chemically modified in a manner that it can no longer act as a guide sequence for efficiently mediating RNA interference and/or be recognized by cellular proteins that facilitate RNAi.

In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein the second sequence is designed or modified in a manner that prevents its entry into the RNAi pathway as a guide sequence or as a sequence that is complementary to a target nucleic acid (e.g., RNA) sequence. Such design or modifications are expected to enhance the activity of siNA and/or improve the specificity of siNA molecules of the invention. These modifications are also expected to minimize any off-target effects and/or associated toxicity.

In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein said second sequence is incapable of acting as a guide sequence for mediating RNA interference.

In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein said second sequence does not have a terminal 5′-hydroxyl(5′-OH) or 5′-phosphate group.

In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein said second sequence comprises a terminal cap moiety at the 5′-end of said second sequence. In one embodiment, the terminal cap moiety comprises an inverted abasic, inverted deoxy abasic, inverted nucleotide moiety, a group shown in FIG. 10, an alkyl or cycloalkyl group, a heterocycle, or any other group that prevents RNAi activity in which the second sequence serves as a guide sequence or template for RNAi.

In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein said second sequence comprises a terminal cap moiety at the 5′-end and 3′-end of said second sequence. In one embodiment, each terminal cap moiety individually comprises an inverted abasic, inverted deoxy abasic, inverted nucleotide moiety, a group shown in FIG. 10, an alkyl or cycloalkyl group, a heterocycle, or any other group that prevents RNAi activity in which the second sequence serves as a guide sequence or template for RNAi.

In one embodiment, the invention features a method for generating siNA molecules of the invention with improved specificity for down regulating or inhibiting the expression of a target nucleic acid (e.g., a DNA or RNA such as a gene or its corresponding RNA), comprising (a) introducing one or more chemical modifications into the structure of a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved specificity. In another embodiment, the chemical modification used to improve specificity comprises terminal cap modifications at the 5′-end, 3′-end, or both 5′ and 3′-ends of the siNA molecule. The terminal cap modifications can comprise, for example, structures shown in FIG. 10 (e.g. inverted deoxyabasic moieties) or any other chemical modification that renders a portion of the siNA molecule (e.g. the sense strand) incapable of mediating RNA interference against an off target nucleic acid sequence. In a non-limiting example, a siNA molecule is designed such that only the antisense sequence of the siNA molecule can serve as a guide sequence for RISC mediated degradation of a corresponding target RNA sequence. This can be accomplished by rendering the sense sequence of the siNA inactive by introducing chemical modifications to the sense strand that preclude recognition of the sense strand as a guide sequence by RNAi machinery. In one embodiment, such chemical modifications comprise any chemical group at the 5′-end of the sense strand of the siNA, or any other group that serves to render the sense strand inactive as a guide sequence for mediating RNA interference. These modifications, for example, can result in a molecule where the 5′-end of the sense strand no longer has a free 5′-hydroxyl(5′-OH) or a free 5′-phosphate group (e.g., phosphate, diphosphate, triphosphate, cyclic phosphate etc.). Non-limiting examples of such siNA constructs are described herein, such as “Stab 9/10”, “Stab 7/8”, “Stab 7/19”, “Stab 17/22”, “Stab 23/24”, and “Stab 24/25” chemistries and variants thereof (see Table IV) wherein the 5′-end and 3′-end of the sense strand of the siNA do not comprise a hydroxyl group or phosphate group.

In one embodiment, the invention features a method for generating siNA molecules of the invention with improved specificity for down regulating or inhibiting the expression of a target nucleic acid (e.g., a DNA or RNA such as a gene or its corresponding RNA), comprising introducing one or more chemical modifications into the structure of a siNA molecule that prevent a strand or portion of the siNA molecule from acting as a template or guide sequence for RNAi activity. In one embodiment, the inactive strand or sense region of the siNA molecule is the sense strand or sense region of the siNA molecule, i.e. the strand or region of the siNA that does not have complementarity to the target nucleic acid sequence. In one embodiment, such chemical modifications comprise any chemical group at the 5′-end of the sense strand or region of the siNA that does not comprise a 5′-hydroxyl(5′-OH) or 5′-phosphate group, or any other group that serves to render the sense strand or sense region inactive as a guide sequence for mediating RNA interference. Non-limiting examples of such siNA constructs are described herein, such as “Stab 9/10”, “Stab 7/8”, “Stab 7/19”, “Stab 17/22”, “Stab 23/24”, and “Stab 24/25” chemistries and variants thereof (see Table IV) wherein the 5′-end and 3′-end of the sense strand of the siNA do not comprise a hydroxyl group or phosphate group.

In one embodiment, the invention features a method for screening siNA molecules that are active in mediating RNA interference against a target nucleic acid sequence comprising (a) generating a plurality of unmodified siNA molecules, (b) screening the siNA molecules of step (a) under conditions suitable for isolating siNA molecules that are active in mediating RNA interference against the target nucleic acid sequence, and (c) introducing chemical modifications (e.g. chemical modifications as described herein or as otherwise known in the art) into the active siNA molecules of (b). In one embodiment, the method further comprises re-screening the chemically modified siNA molecules of step (c) under conditions suitable for isolating chemically modified siNA molecules that are active in mediating RNA interference against the target nucleic acid sequence.

In one embodiment, the invention features a method for screening chemically modified siNA molecules that are active in mediating RNA interference against a target nucleic acid sequence comprising (a) generating a plurality of chemically modified siNA molecules (e.g. siNA molecules as described herein or as otherwise known in the art), and (b) screening the siNA molecules of step (a) under conditions suitable for isolating chemically modified siNA molecules that are active in mediating RNA interference against the target nucleic acid sequence.

The term “ligand” refers to any compound or molecule, such as a drug, peptide, hormone, or neurotransmitter, that is capable of interacting with another compound, such as a receptor, either directly or indirectly. The receptor that interacts with a ligand can be present on the surface of a cell or can alternately be an intercullular receptor. Interaction of the ligand with the receptor can result in a biochemical reaction, or can simply be a physical interaction or association.

In another embodiment, the invention features a method for generating siNA molecules of the invention with improved bioavailability comprising (a) introducing an excipient formulation to a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved bioavailability. Such excipients include polymers such as cyclodextrins, lipids, cationic lipids, polyamines, phospholipids, nanoparticles, receptors, ligands, and others.

In another embodiment, the invention features a method for generating siNA molecules of the invention with improved bioavailability comprising (a) introducing nucleotides having any of Formulae I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved bioavailability.

In another embodiment, polyethylene glycol (PEG) can be covalently attached to siNA compounds of the present invention. The attached PEG can be any molecular weight, preferably from about 2,000 to about 50,000 daltons (Da).

The present invention can be used alone or as a component of a kit having at least one of the reagents necessary to carry out the in vitro or in vivo introduction of RNA to test samples and/or subjects. For example, preferred components of the kit include a siNA molecule of the invention and a vehicle that promotes introduction of the siNA into cells of interest as described herein (e.g., using lipids and other methods of transfection known in the art, see for example Beigelman et al, U.S. Pat. No. 6,395,713). The kit can be used for target validation, such as in determining gene function and/or activity, or in drug optimization, and in drug discovery (see for example Usman et al., U.S. Ser. No. 60/402,996). Such a kit can also include instructions to allow a user of the kit to practice the invention.

The term “short interfering nucleic acid”, “siNA”, “short interfering RNA”, “siRNA”, “short interfering nucleic acid molecule”, “short interfering oligonucleotide molecule”, or “chemically-modified short interfering nucleic acid molecule” as used herein refers to any nucleic acid molecule capable of inhibiting or down regulating gene expression or viral replication, for example by mediating RNA interference “RNAi” or gene silencing in a sequence-specific manner; see for example Zamore et al., 2000, Cell, 101, 25-33; Bass, 2001, Nature, 411, 428-429; Elbashir et al., 2001, Nature, 411, 494-498; and Kreutzer et al., International PCT Publication No. WO 00/44895; Zernicka-Goetz et al., International PCT Publication No. WO 01/36646; Fire, International PCT Publication No. WO 99/32619; Plaetinck et al., International PCT Publication No. WO 00/01846; Mello and Fire, International PCT Publication No. WO 01/29058; Deschamps-Depaillette, International PCT Publication No. WO 99/07409; and Li et al., International PCT Publication No. WO 00/44914; Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237; Hutvagner and Zamore, 2002, Science, 297, 2056-60; McManus et al., 2002, RNA, 8, 842-850; Reinhart et al., 2002, Gene & Dev., 16, 1616-1626; and Reinhart & Bartel, 2002, Science, 297, 1831). Non limiting examples of siNA molecules of the invention are shown in FIGS. 4-6, and Tables II and III herein. For example the siNA can be a double-stranded polynucleotide molecule comprising self-complementary sense and antisense regions, wherein the antisense region comprises nucleotide sequence that is complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof and the sense region having nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof. The siNA can be assembled from two separate oligonucleotides, where one strand is the sense strand and the other is the antisense strand, wherein the antisense and sense strands are self-complementary (i.e. each strand comprises nucleotide sequence that is complementary to nucleotide sequence in the other strand; such as where the antisense strand and sense strand form a duplex or double stranded structure, for example wherein the double stranded region is about 19 base pairs); the antisense strand comprises nucleotide sequence that is complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof and the sense strand comprises nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof. Alternatively, the siNA is assembled from a single oligonucleotide, where the self-complementary sense and antisense regions of the siNA are linked by means of a nucleic acid based or non-nucleic acid-based linker(s). The siNA can be a polynucleotide with a duplex, asymmetric duplex, hairpin or asymmetric hairpin secondary structure, having self-complementary sense and antisense regions, wherein the antisense region comprises nucleotide sequence that is complementary to nucleotide sequence in a separate target nucleic acid molecule or a portion thereof and the sense region having nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof. The siNA can be a circular single-stranded polynucleotide having two or more loop structures and a stem comprising self-complementary sense and antisense regions, wherein the antisense region comprises nucleotide sequence that is complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof and the sense region having nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof, and wherein the circular polynucleotide can be processed either in vivo or in vitro to generate an active siNA molecule capable of mediating RNAi. The siNA can also comprise a single stranded polynucleotide having nucleotide sequence complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof (for example, where such siNA molecule does not require the presence within the siNA molecule of nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof), wherein the single stranded polynucleotide can further comprise a terminal phosphate group, such as a 5′-phosphate (see for example Martinez et al., 2002, Cell., 110, 563-574 and Schwarz et al., 2002, Molecular Cell, 10, 537-568), or 5′,3′-diphosphate. In certain embodiments, the siNA molecule of the invention comprises separate sense and antisense sequences or regions, wherein the sense and antisense regions are covalently linked by nucleotide or non-nucleotide linkers molecules as is known in the art, or are alternately non-covalently linked by ionic interactions, hydrogen bonding, van der waals interactions, hydrophobic interactions, and/or stacking interactions. In certain embodiments, the siNA molecules of the invention comprise nucleotide sequence that is complementary to nucleotide sequence of a target gene. In another embodiment, the siNA molecule of the invention interacts with nucleotide sequence of a target gene in a manner that causes inhibition of expression of the target gene. As used herein, siNA molecules need not be limited to those molecules containing only RNA, but further encompasses chemically-modified nucleotides and non-nucleotides. In certain embodiments, the short interfering nucleic acid molecules of the invention lack 2′-hydroxy(2′-OH) containing nucleotides. Applicant describes in certain embodiments short interfering nucleic acids that do not require the presence of nucleotides having a 2′-hydroxy group for mediating RNAi and as such, short interfering nucleic acid molecules of the invention optionally do not include any ribonucleotides (e.g., nucleotides having a 2′-OH group). Such siNA molecules that do not require the presence of ribonucleotides within the siNA molecule to support RNAi can however have an attached linker or linkers or other attached or associated groups, moieties, or chains containing one or more nucleotides with 2′-OH groups. Optionally, siNA molecules can comprise ribonucleotides at about 5, 10, 20, 30, 40, or 50% of the nucleotide positions. The modified short interfering nucleic acid molecules of the invention can also be referred to as short interfering modified oligonucleotides “siMON.” As used herein, the term siNA is meant to be equivalent to other terms used to describe nucleic acid molecules that are capable of mediating sequence specific RNAi, for example short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), short hairpin RNA (shRNA), short interfering oligonucleotide, short interfering nucleic acid, short interfering modified oligonucleotide, chemically-modified siRNA, post-transcriptional gene silencing RNA (ptgsRNA), and others. In addition, as used herein, the term RNAi is meant to be equivalent to other terms used to describe sequence specific RNA interference, such as post transcriptional gene silencing, translational inhibition, or epigenetics. For example, siNA molecules of the invention can be used to epigenetically silence genes at both the post-transcriptional level or the pre-transcriptional level. In a non-limiting example, epigenetic regulation of gene expression by siNA molecules of the invention can result from siNA mediated modification of chromatin structure or methylation pattern to alter gene expression (see, for example, Verdel et al., 2004, Science, 303, 672-676; Pal-Bhadra et al., 2004, Science, 303, 669-672; Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237).

In one embodiment, a siNA molecule of the invention is a duplex forming oligonucleotide “DFO”, (see for example FIGS. 14-15 and Vaish et al., U.S. Ser. No. 10/727,780 filed Dec. 3, 2003 and International PCT Application No. US04/16390, filed May 24, 2004).

In one embodiment, a siNA molecule of the invention is a multifunctional siNA, (see for example FIGS. 16-21 and Jadhav et al., U.S. Ser. No. 60/543,480 filed Feb. 10, 2004 and International PCT Application No. US04/16390, filed May 24, 2004). The multifunctional siNA of the invention can comprise sequence targeting, for example, two regions of BACE RNA (see for example target sequences in Tables II and III).

By “asymmetric hairpin” as used herein is meant a linear siNA molecule comprising an antisense region, a loop portion that can comprise nucleotides or non-nucleotides, and a sense region that comprises fewer nucleotides than the antisense region to the extent that the sense region has enough complementary nucleotides to base pair with the antisense region and form a duplex with loop. For example, an asymmetric hairpin siNA molecule of the invention can comprise an antisense region having length sufficient to mediate RNAi in a cell or in vitro system (e.g. about 19 to about 22, or about 19, 20, 21, or 22 nucleotides) and a loop region comprising about 4 to about 8 (e.g., about 4, 5, 6, 7, or 8) nucleotides, and a sense region having about 3 to about 18 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18) nucleotides that are complementary to the antisense region. The asymmetric hairpin siNA molecule can also comprise a 5′-terminal phosphate group that can be chemically modified. The loop portion of the asymmetric hairpin siNA molecule can comprise nucleotides, non-nucleotides, linker molecules, or conjugate molecules as described herein.

By “asymmetric duplex” as used herein is meant a siNA molecule having two separate strands comprising a sense region and an antisense region, wherein the sense region comprises fewer nucleotides than the antisense region to the extent that the sense region has enough complementary nucleotides to base pair with the antisense region and form a duplex. For example, an asymmetric duplex siNA molecule of the invention can comprise an antisense region having length sufficient to mediate RNAi in a cell or in vitro system e.g. about 19 to about 22 (e.g. about 19, 20, 21, or 22) nucleotides and a sense region having about 3 to about 18 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18) nucleotides that are complementary to the antisense region.

By “modulate” is meant that the expression of the gene, or level of RNA molecule or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits is up regulated or down regulated, such that expression, level, or activity is greater than or less than that observed in the absence of the modulator. For example, the term “modulate” can mean “inhibit,” but the use of the word “modulate” is not limited to this definition.

By “inhibit”, “down-regulate”, or “reduce”, it is meant that the expression of the gene, or level of RNA molecules or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits, is reduced below that observed in the absence of the nucleic acid molecules (e.g., siNA) of the invention. In one embodiment, inhibition, down-regulation or reduction with an siNA molecule is below that level observed in the presence of an inactive or attenuated molecule. In another embodiment, inhibition, down-regulation, or reduction with siNA molecules is below that level observed in the presence of, for example, an siNA molecule with scrambled sequence or with mismatches. In another embodiment, inhibition, down-regulation, or reduction of gene expression with a nucleic acid molecule of the instant invention is greater in the presence of the nucleic acid molecule than in its absence. In one embodiment, inhibition, down regulation, or reduction of gene expression is associated with post transcriptional silencing, such as RNAi mediated cleavage of a target nucleic acid molecule (e.g. RNA) or inhibition of translation. In one embodiment, inhibition, down regulation, or reduction of gene expression is associated with pretranscriptional silencing.

By “gene”, or “target gene”, is meant, a nucleic acid that encodes an RNA, for example, nucleic acid sequences including, but not limited to, structural genes encoding a polypeptide. A gene or target gene can also encode a functional RNA (fRNA) or non-coding RNA (ncRNA), such as small temporal RNA (stRNA), micro RNA (miRNA), small nuclear RNA (snRNA), short interfering RNA (siRNA), small nucleolar RNA (snRNA), ribosomal RNA (rRNA), transfer RNA (tRNA) and precursor RNAs thereof. Such non-coding RNAs can serve as target nucleic acid molecules for siNA mediated RNA interference in modulating the activity of fRNA or ncRNA involved in functional or regulatory cellular processes. Abberant fRNA or ncRNA activity leading to disease can therefore be modulated by siNA molecules of the invention. siNA molecules targeting fRNA and ncRNA can also be used to manipulate or alter the genotype or phenotype of a subject, organism or cell, by intervening in cellular processes such as genetic imprinting, transcription, translation, or nucleic acid processing (e.g., transamination, methylation etc.). The target gene can be a gene derived from a cell, an endogenous gene, a transgene, or exogenous genes such as genes of a pathogen, for example a virus, which is present in the cell after infection thereof. The cell containing the target gene can be derived from or contained in any organism, for example a plant, animal, protozoan, virus, bacterium, or fungus. Non-limiting examples of plants include monocots, dicots, or gymnosperms. Non-limiting examples of animals include vertebrates or invertebrates. Non-limiting examples of fungi include molds or yeasts. For a review, see for example Snyder and Gerstein, 2003, Science, 300, 258-260.

By “non-canonical base pair” is meant any non-Watson Crick base pair, such as mismatches and/or wobble base pairs, inlcuding flipped mismatches, single hydrogen bond mismatches, trans-type mismatches, triple base interactions, and quadruple base interactions. Non-limiting examples of such non-canonical base pairs include, but are not limited to, AC reverse Hoogsteen, AC wobble, AU reverse Hoogsteen, GU wobble, AA N7 amino, CC 2-carbonyl-amino(H1)-N3-amino(H2), GA sheared, UC 4-carbonyl-amino, UU imino-carbonyl, AC reverse wobble, AU Hoogsteen, AU reverse Watson Crick, CG reverse Watson Crick, GC N3-amino-amino N3, AA N1-amino symmetric, AA N7-amino symmetric, GA N7-N1 amino-carbonyl, GA+ carbonyl-amino N7-N1, GG N1-carbonyl symmetric, GG N3-amino symmetric, CC carbonyl-amino symmetric, CC N3-amino symmetric, UU 2-carbonyl-imino symmetric, UU 4-carbonyl-imino symmetric, AA amino-N3, AA N1-amino, AC amino 2-carbonyl, AC N3-amino, AC N7-amino, AU amino-4-carbonyl, AU N1-imino, AU N3-imino, AU N7-imino, CC carbonyl-amino, GA amino-N1, GA amino-N7, GA carbonyl-amino, GA N3-amino, GC amino-N3, GC carbonyl-amino, GC N3-amino, GC N7-amino, GG amino-N7, GG carbonyl-imino, GG N7-amino, GU amino-2-carbonyl, GU carbonyl-imino, GU imino-2-carbonyl, GU N7-imino, psiU imino-2-carbonyl, UC 4-carbonyl-amino, UC imino-carbonyl, UU imino-4-carbonyl, AC C2-H—N3, GA carbonyl-C2-H, UU imino-4-carbonyl 2 carbonyl-C5-H, AC amino(A) N3(C)-carbonyl, GC imino amino-carbonyl, Gpsi imino-2-carbonyl amino-2-carbonyl, and GU imino amino-2-carbonyl base pairs.

By “BACE” or “beta secretase”as used herein is meant, BACE protein, peptide, or polypeptide having beta-secretase activity, such as that involved in generating beta-amyloid, for example, sequences encoded by BACE Genbank Accession Nos. shown in Table I. The term BACE also refers to nucleic acid sequences encoding any BACE protein, peptide, or polypeptide having BACE activity. The term “BACE” is also meant to include other BACE encoding sequence, such as BACE isoforms, mutant BACE genes, splice variants of BACE genes, and BACE gene polymorphisms.

By “APP” or “amyloid precursor protein” as used herein is meant any protein, peptide, or polypeptide that is processed to generate beta-amyloid. The term APP also refers to sequences that encode APP protein, for example, Genbank Accession Nos. shown in Table I. The term APP also refers to nucleic acid sequences encoding any APP protein, peptide, or polypeptide having APP activity. The term “APP” is also meant to include other APP encoding sequence, such as APP isoforms, mutant APP genes, splice variants of APP, and APP gene polymorphisms.

By “presenillin” or “PS”, i.e., “PS-1” or “PS-2”, or “PSEN”, i.e., “PSEN1” or “PSEN2”, as used herein is meant any protein, peptide, or polypeptide having gamma-secretase activity, such as that involved in generating beta-amyloid. The term PS also refers to sequences that encode presenillin protein, for example, PS-1 or PS-2, (i.e., Genbank Accession Nos. shown in Table I). The term “PS”, for example, “PS-1” or “PS-2”, also refers to nucleic acid sequences encoding any PS protein, peptide, or polypeptide having PS activity. The term “PS”, for example, “PS-1” or “PS-2”, is also meant to include other PS encoding sequence, such as PS isoforms, mutant PS genes, splice variants of PS, and PS gene polymorphisms.

By “PIN-1” as used herein is meant any protein, peptide, or polypeptide having peptidyl-prolyl cis/trans isomerase activity, such as those involved in the development of Neurofibrillary Tangles. The term PIN-1 also refers to sequences that encode PIN-1 protein, i.e., Genbank Accession Nos. shown in Table I. The term PIN-1 also refers to nucleic acid sequences encoding any PIN-1 protein, peptide, or polypeptide having PIN-1 activity. The term “PIN-1” is also meant to include other PIN-1 encoding sequence, such as PIN-1 isoforms, mutant PIN-1 genes, splice variants of PIN-1, and PIN-1 gene polymorphisms.

Furthermore, as discussed previously, all embodiments, compositions, methods, and uses described herein using BACE as an examplery gene are equally applicable to APP, PIN-1, and PS (i.e., PS-1, and PS-2) genes.

By “homologous sequence” is meant, a nucleotide sequence that is shared by one or more polynucleotide sequences, such as genes, gene transcripts and/or non-coding polynucleotides. For example, a homologous sequence can be a nucleotide sequence that is shared by two or more genes encoding related but different proteins, such as different members of a gene family, different protein epitopes, different protein isoforms or completely divergent genes, such as a cytokine and its corresponding receptors. A homologous sequence can be a nucleotide sequence that is shared by two or more non-coding polynucleotides, such as noncoding DNA or RNA, regulatory sequences, introns, and sites of transcriptional control or regulation. Homologous sequences can also include conserved sequence regions shared by more than one polynucleotide sequence. Homology does not need to be perfect homology (e.g., 100%), as partially homologous sequences are also contemplated by the instant invention (e.g., 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80% etc.).

By “conserved sequence region” is meant, a nucleotide sequence of one or more regions in a polynucleotide does not vary significantly between generations or from one biological system, subject, or organism to another biological system, subject, or organism. The polynucleotide can include both coding and non-coding DNA and RNA.

By “sense region” is meant a nucleotide sequence of a siNA molecule having complementarity to an antisense region of the siNA molecule. In addition, the sense region of a siNA molecule can comprise a nucleic acid sequence having homology with a target nucleic acid sequence.

By “antisense region” is meant a nucleotide sequence of a siNA molecule having complementarity to a target nucleic acid sequence. In addition, the antisense region of a siNA molecule can optionally comprise a nucleic acid sequence having complementarity to a sense region of the siNA molecule.

By “target nucleic acid” is meant any nucleic acid sequence whose expression or activity is to be modulated. The target nucleic acid can be DNA or RNA.

By “complementarity” is meant that a nucleic acid can form hydrogen bond(s) with another nucleic acid sequence by either traditional Watson-Crick or other non-traditional types. In reference to the nucleic molecules of the present invention, the binding free energy for a nucleic acid molecule with its complementary sequence is sufficient to allow the relevant function of the nucleic acid to proceed, e.g., RNAi activity. Determination of binding free energies for nucleic acid molecules is well known in the art (see, e.g., Turner et al., 1987, CSH Symp. Quant. Biol. LII pp. 123-133; Frier et al., 1986, Proc. Nat. Acad. Sci. USA 83:9373-9377; Turner et al., 1987, J. Am. Chem. Soc. 109:3783-3785). A percent complementarity indicates the percentage of contiguous residues in a nucleic acid molecule that can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, or 10 nucleotides out of a total of 10 nucleotides in the first oligonucleotide being based paired to a second nucleic acid sequence having 10 nucleotides represents 50%, 60%, 70%, 80%, 90%, and 100% complementary respectively). “Perfectly complementary” means that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence.

In one embodiment, siNA molecules of the invention that down regulate or reduce BACE gene expression are used for treating Alzheimer's disease in a subject or organism.

In one embodiment, the siNA molecules of the invention are used to treat neurodegenerative disorders or conditions, such as dementia, and stroke/cardiovascular accident in a subject or organism.

In one embodiment of the present invention, each sequence of a siNA molecule of the invention is independently about 18 to about 24 nucleotides in length, in specific embodiments about 18, 19, 20, 21, 22, 23, or 24 nucleotides in length. In another embodiment, the siNA duplexes of the invention independently comprise about 17 to about 23 base pairs (e.g., about 17, 18, 19, 20, 21, 22, or 23). In yet another embodiment, siNA molecules of the invention comprising hairpin or circular structures are about 35 to about 55 (e.g., about 35, 40, 45, 50 or 55) nucleotides in length, or about 38 to about 44 (e.g., about 38, 39, 40, 41, 42, 43, or 44) nucleotides in length and comprising about 16 to about 22 (e.g., about 16, 17, 18, 19, 20, 21 or 22) base pairs. Exemplary siNA molecules of the invention are shown in Table H. Exemplary synthetic siNA molecules of the invention are shown in Table m and/or FIGS. 4-5.

As used herein “cell” is used in its usual biological sense, and does not refer to an entire multicellular organism, e.g., specifically does not refer to a human. The cell can be present in an organism, e.g., birds, plants and mammals such as humans, cows, sheep, apes, monkeys, swine, dogs, and cats. The cell can be prokaryotic (e.g., bacterial cell) or eukaryotic (e.g., mammalian or plant cell). The cell can be of somatic or germ line origin, totipotent or pluripotent, dividing or non-dividing. The cell can also be derived from or can comprise a gamete or embryo, a stem cell, or a fully differentiated cell.

The siNA molecules of the invention are added directly, or can be complexed with cationic lipids, packaged within liposomes, or otherwise delivered to target cells or tissues. The nucleic acid or nucleic acid complexes can be locally administered to relevant tissues ex vivo, or in vivo through direct dermal application, transdermal application, or injection, with or without their incorporation in biopolymers. In particular embodiments, the nucleic acid molecules of the invention comprise sequences shown in Tables II-III and/or FIGS. 4-5. Examples of such nucleic acid molecules consist essentially of sequences defined in these tables and figures. Furthermore, the chemically modified constructs described in Table IV can be applied to any siNA sequence of the invention.

In another aspect, the invention provides mammalian cells containing one or more siNA molecules of this invention. The one or more siNA molecules can independently be targeted to the same or different sites.

By “RNA” is meant a molecule comprising at least one ribonucleotide residue. By “ribonucleotide” is meant a nucleotide with a hydroxyl group at the 2′ position of a β-D-ribofuranose moiety. The terms include double-stranded RNA, single-stranded RNA, isolated RNA such as partially purified RNA, essentially pure RNA, synthetic RNA, recombinantly produced RNA, as well as altered RNA that differs from naturally occurring RNA by the addition, deletion, substitution and/or alteration of one or more nucleotides. Such alterations can include addition of non-nucleotide material, such as to the end(s) of the siNA or internally, for example at one or more nucleotides of the RNA. Nucleotides in the RNA molecules of the instant invention can also comprise non-standard nucleotides, such as non-naturally occurring nucleotides or chemically synthesized nucleotides or deoxynucleotides. These altered RNAs can be referred to as analogs or analogs of naturally-occurring RNA.

By “subject” is meant an organism, which is a donor or recipient of explanted cells or the cells themselves. “Subject” also refers to an organism to which the nucleic acid molecules of the invention can be administered. A subject can be a mammal or mammalian cells, including a human or human cells.

The term “phosphorothioate” as used herein refers to an internucleotide linkage having Formula I, wherein Z and/or W comprise a sulfur atom. Hence, the term phosphorothioate refers to both phosphorothioate and phosphorodithioate internucleotide linkages.

The term “phosphonoacetate” as used herein refers to an internucleotide linkage having Formula I, wherein Z and/or W comprise an acetyl or protected acetyl group.

The term “thiophosphonoacetate” as used herein refers to an internucleotide linkage having Formula I, wherein Z comprises an acetyl or protected acetyl group and W comprises a sulfur atom or alternately W comprises an acetyl or protected acetyl group and Z comprises a sulfur atom.

The term “universal base” as used herein refers to nucleotide base analogs that form base pairs with each of the natural DNA/RNA bases with little discrimination between them. Non-limiting examples of universal bases include C-phenyl, C-naphthyl and other aromatic derivatives, inosine, azole carboxamides, and nitroazole derivatives such as 3-nitropyrrole, 4-nitroindole, 5-nitroindole, and 6-nitroindole as known in the art (see for example Loakes, 2001, Nucleic Acids Research, 29, 2437-2447).

The term “acyclic nucleotide” as used herein refers to any nucleotide having an acyclic ribose sugar, for example where any of the ribose carbons (C1, C2, C3, C4, or C5), are independently or in combination absent from the nucleotide.

The nucleic acid molecules of the instant invention, individually, or in combination or in conjunction with other drugs, can be used to for preventing or treating Alzheimer's disease and other neurodegenerative disorders or conditions, such as dementia and stroke/cardiovascular accident in a subject or organism.

For example, the siNA molecules can be administered to a subject or can be administered to other appropriate cells evident to those skilled in the art, individually or in combination with one or more drugs under conditions suitable for the treatment.

In a further embodiment, the siNA molecules can be used in combination with other known treatments to prevent or treat Alzheimer's disease and other neurodegenerative disorders or conditions, such as dementia and stroke/cardiovascular accident in a subject or organism. For example, the described molecules could be used in combination with one or more known compounds, treatments, or procedures to prevent or treat Alzheimer's disease and other neurodegenerative disorders or conditions, such as dementia and stroke/cardiovascular accident in a subject or organism as are known in the art.

In one embodiment, the invention features an expression vector comprising a nucleic acid sequence encoding at least one siNA molecule of the invention, in a manner which allows expression of the siNA molecule. For example, the vector can contain sequence(s) encoding both strands of a siNA molecule comprising a duplex. The vector can also contain sequence(s) encoding a single nucleic acid molecule that is self-complementary and thus forms a siNA molecule. Non-limiting examples of such expression vectors are described in Paul et al., 2002, Nature Biotechnology, 19, 505; Miyagishi and Taira, 2002, Nature Biotechnology, 19, 497; Lee et al., 2002, Nature Biotechnology, 19, 500; and Novina et al., 2002, Nature Medicine, advance online publication doi:10.1038/nm725.

In another embodiment, the invention features a mammalian cell, for example, a human cell, including an expression vector of the invention.

In yet another embodiment, the expression vector of the invention comprises a sequence for a siNA molecule having complementarity to a RNA molecule referred to by a Genbank Accession numbers, for example Genbank Accession Nos. shown in Table I.

In one embodiment, an expression vector of the invention comprises a nucleic acid sequence encoding two or more siNA molecules, which can be the same or different.

In another aspect of the invention, siNA molecules that interact with target RNA molecules and down-regulate gene encoding target RNA molecules (for example target RNA molecules referred to by Genbank Accession numbers herein) are expressed from transcription units inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. siNA expressing viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. The recombinant vectors capable of expressing the siNA molecules can be delivered as described herein, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of siNA molecules. Such vectors can be repeatedly administered as necessary. Once expressed, the siNA molecules bind and down-regulate gene function or expression via RNA interference (RNAi). Delivery of siNA expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell.

By “vectors” is meant any nucleic acid- and/or viral-based technique used to deliver a desired nucleic acid

Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a non-limiting example of a scheme for the synthesis of siNA molecules. The complementary siNA sequence strands, strand 1 and strand 2, are synthesized in tandem and are connected by a cleavable linkage, such as a nucleotide succinate or abasic succinate, which can be the same or different from the cleavable linker used for solid phase synthesis on a solid support. The synthesis can be either solid phase or solution phase, in the example shown, the synthesis is a solid phase synthesis. The synthesis is performed such that a protecting group, such as a dimethoxytrityl group, remains intact on the terminal nucleotide of the tandem oligonucleotide. Upon cleavage and deprotection of the oligonucleotide, the two siNA strands spontaneously hybridize to form a siNA duplex, which allows the purification of the duplex by utilizing the properties of the terminal protecting group, for example by applying a trityl on purification method wherein only duplexes/oligonucleotides with the terminal protecting group are isolated.

FIG. 2 shows a MALDI-TOF mass spectrum of a purified siNA duplex synthesized by a method of the invention. The two peaks shown correspond to the predicted mass of the separate siNA sequence strands. This result demonstrates that the siNA duplex generated from tandem synthesis can be purified as a single entity using a simple trityl-on purification methodology.

FIG. 3 shows a non-limiting proposed mechanistic representation of target RNA degradation involved in RNAi. Double-stranded RNA (dsRNA), which is generated by RNA-dependent RNA polymerase (RdRP) from foreign single-stranded RNA, for example viral, transposon, or other exogenous RNA, activates the DICER enzyme that in turn generates siNA duplexes. Alternately, synthetic or expressed siNA can be introduced directly into a cell by appropriate means. An active siNA complex forms which recognizes a target RNA, resulting in degradation of the target RNA by the RISC endonuclease complex or in the synthesis of additional RNA by RNA-dependent RNA polymerase (RdRP), which can activate DICER and result in additional siNA molecules, thereby amplifying the RNAi response.

FIG. 4A-F shows non-limiting examples of chemically-modified siNA constructs of the present invention. In the figure, N stands for any nucleotide (adenosine, guanosine, cytosine, uridine, or optionally thymidine, for example thymidine can be substituted in the overhanging regions designated by parenthesis (N N). Various modifications are shown for the sense and antisense strands of the siNA constructs.

FIG. 4A: The sense strand comprises 21 nucleotides wherein the two terminal 3′-nucleotides are optionally base paired and wherein all nucleotides present are ribonucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, and wherein all nucleotides present are ribonucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s”, optionally connects the (N N) nucleotides in the antisense strand.

FIG. 4B: The sense strand comprises 21 nucleotides wherein the two terminal 3′-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2′deoxy-2′-fluoro modified nucleotides and all purine nucleotides that may be present are 2′-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety and wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides and all purine nucleotides that may be present are 2′-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s”, optionally connects the (N N) nucleotides in the sense and antisense strand.

FIG. 4C: The sense strand comprises 21 nucleotides having 5′- and 3′-terminal cap moieties wherein the two terminal 3′-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2′-O-methyl or 2′-deoxy-2′-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety and wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s”, optionally connects the (N N) nucleotides in the antisense strand.

FIG. 4D: The sense strand comprises 21 nucleotides having 5′- and 3′-terminal cap moieties wherein the two terminal 3′-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein and wherein and all purine nucleotides that may be present are 2′-deoxy nucleotides. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety and wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides and all purine nucleotides that may be present are 2′-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s”, optionally connects the (N N) nucleotides in the antisense strand.

FIG. 4E: The sense strand comprises 21 nucleotides having 5′- and 3′-terminal cap moieties wherein the two terminal 3′-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety and wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides and all purine nucleotides that may be present are 2′-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s”, optionally connects the (N N) nucleotides in the antisense strand.

FIG. 4F: The sense strand comprises 21 nucleotides having 5′- and 3′-terminal cap moieties wherein the two terminal 3′-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein and wherein and all purine nucleotides that may be present are 2′-deoxy nucleotides. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety and wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, and having one 3′-terminal phosphorothioate internucleotide linkage and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides and all purine nucleotides that may be present are 2′-deoxy nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s”, optionally connects the (N N) nucleotides in the antisense strand. The antisense strand of constructs A-F comprise sequence complementary to any target nucleic acid sequence of the invention. Furthermore, when a glyceryl moiety (L) is present at the 3′-end of the antisense strand for any construct shown in FIG. 4 A-F, the modified internucleotide linkage is optional.

FIG. 5A-F shows non-limiting examples of specific chemically-modified siNA sequences of the invention. A-F applies the chemical modifications described in FIG. 4A-F to a BACE siNA sequence. Such chemical modifications can be applied to any BACE sequence and/or BACE polymorphism sequence.

FIG. 6 shows non-limiting examples of different siNA constructs of the invention. The examples shown (constructs 1, 2, and 3) have 19 representative base pairs; however, different embodiments of the invention include any number of base pairs described herein. Bracketed regions represent nucleotide overhangs, for example, comprising about 1, 2, 3, or 4 nucleotides in length, preferably about 2 nucleotides. Constructs 1 and 2 can be used independently for RNAi activity. Construct 2 can comprise a polynucleotide or non-nucleotide linker, which can optionally be designed as a biodegradable linker. In one embodiment, the loop structure shown in construct 2 can comprise a biodegradable linker that results in the formation of construct 1 in vivo and/or in vitro. In another example, construct 3 can be used to generate construct 2 under the same principle wherein a linker is used to generate the active siNA construct 2 in vivo and/or in vitro, which can optionally utilize another biodegradable linker to generate the active siNA construct 1 in vivo and/or in vitro. As such, the stability and/or activity of the siNA constructs can be modulated based on the design of the siNA construct for use in vivo or in vitro and/or in vitro.

FIG. 7A-C is a diagrammatic representation of a scheme utilized in generating an expression cassette to generate siNA hairpin constructs.

FIG. 7A: A DNA oligomer is synthesized with a 5′-restriction site (R1) sequence followed by a region having sequence identical (sense region of siNA) to a predetermined BACE target sequence, wherein the sense region comprises, for example, about 19, 20, 21, or 22 nucleotides (N) in length, which is followed by a loop sequence of defined sequence (X), comprising, for example, about 3 to about 10 nucleotides.

FIG. 7B: The synthetic construct is then extended by DNA polymerase to generate a hairpin structure having self-complementary sequence that will result in a siNA transcript having specificity for a BACE target sequence and having self-complementary sense and antisense regions.

FIG. 7C: The construct is heated (for example to about 95° C.) to linearize the sequence, thus allowing extension of a complementary second DNA strand using a primer to the 3′-restriction sequence of the first strand. The double-stranded DNA is then inserted into an appropriate vector for expression in cells. The construct can be designed such that a 3′-terminal nucleotide overhang results from the transcription, for example, by engineering restriction sites and/or utilizing a poly-U termination region as described in Paul et al., 2002, Nature Biotechnology, 29, 505-508.

FIG. 8A-C is a diagrammatic representation of a scheme utilized in generating an expression cassette to generate double-stranded siNA constructs.

FIG. 8A: A DNA oligomer is synthesized with a 5′-restriction (R1) site sequence followed by a region having sequence identical (sense region of siNA) to a predetermined BACE target sequence, wherein the sense region comprises, for example, about 19, 20, 21, or 22 nucleotides (N) in length, and which is followed by a 3′-restriction site (R2) which is adjacent to a loop sequence of defined sequence (X).

FIG. 8B: The synthetic construct is then extended by DNA polymerase to generate a hairpin structure having self-complementary sequence.

FIG. 8C: The construct is processed by restriction enzymes specific to R1 and R2 to generate a double-stranded DNA which is then inserted into an appropriate vector for expression in cells. The transcription cassette is designed such that a U6 promoter region flanks each side of the dsDNA which generates the separate sense and antisense strands of the siNA. Poly T termination sequences can be added to the constructs to generate U overhangs in the resulting transcript.

FIG. 9A-E is a diagrammatic representation of a method used to determine target sites for siNA mediated RNAi within a particular target nucleic acid sequence, such as messenger RNA.

FIG. 9A: A pool of siNA oligonucleotides are synthesized wherein the antisense region of the siNA constructs has complementarity to target sites across the target nucleic acid sequence, and wherein the sense region comprises sequence complementary to the antisense region of the siNA.

FIGS. 9B&C: (FIG. 9B) The sequences are pooled and are inserted into vectors such that (FIG. 9C) transfection of a vector into cells results in the expression of the siNA.

FIG. 9D: Cells are sorted based on phenotypic change that is associated with modulation of the target nucleic acid sequence.

FIG. 9E: The siNA is isolated from the sorted cells and is sequenced to identify efficacious target sites within the target nucleic acid sequence.

FIG. 10 shows non-limiting examples of different stabilization chemistries (1-10) that can be used, for example, to stabilize the 3′-end of siNA sequences of the invention, including (1) [3-3′]-inverted deoxyribose; (2) deoxyribonucleotide; (3) [5′-3′]-3′-deoxyribonucleotide; (4) [5′-3′]-ribonucleotide; (5) [5′-3′]-3′-O-methyl ribonucleotide; (6) 3′-glyceryl; (7) [3′-5′]-3′-deoxyribonucleotide; (8) [3′-3′]-deoxyribonucleotide; (9) [5′-2′]-deoxyribonucleotide; and (10) [5-3′]-dideoxyribonucleotide. In addition to modified and unmodified backbone chemistries indicated in the figure, these chemistries can be combined with different backbone modifications as described herein, for example, backbone modifications having Formula I. In addition, the 2′-deoxy nucleotide shown 5′ to the terminal modifications shown can be another modified or unmodified nucleotide or non-nucleotide described herein, for example modifications having any of Formulae I-VII or any combination thereof.

FIG. 11 shows a non-limiting example of a strategy used to identify chemically modified siNA constructs of the invention that are nuclease resistance while preserving the ability to mediate RNAi activity. Chemical modifications are introduced into the siNA construct based on educated design parameters (e.g. introducing 2′-mofications, base modifications, backbone modifications, terminal cap modifications etc). The modified construct in tested in an appropriate system (e.g. human serum for nuclease resistance, shown, or an animal model for PK/delivery parameters). In parallel, the siNA construct is tested for RNAi activity, for example in a cell culture system such as a luciferase reporter assay). Lead siNA constructs are then identified which possess a particular characteristic while maintaining RNAi activity, and can be further modified and assayed once again. This same approach can be used to identify siNA-conjugate molecules with improved pharmacokinetic profiles, delivery, and RNAi activity.

FIG. 12 shows non-limiting examples of phosphorylated siNA molecules of the invention, including linear and duplex constructs and asymmetric derivatives thereof.

FIG. 13 shows non-limiting examples of chemically modified terminal phosphate groups of the invention.

FIG. 14A shows a non-limiting example of methodology used to design self complementary DFO constructs utilizing palidrome and/or repeat nucleic acid sequences that are identified in a target nucleic acid sequence. (i) A palindrome or repeat sequence is identified in a nucleic acid target sequence. (ii) A sequence is designed that is complementary to the target nucleic acid sequence and the palindrome sequence. (iii) An inverse repeat sequence of the non-palindrome/repeat portion of the complementary sequence is appended to the 3′-end of the complementary sequence to generate a self complementary DFO molecule comprising sequence complementary to the nucleic acid target. (iv) The DFO molecule can self-assemble to form a double stranded oligonucleotide. FIG. 14B shows a non-limiting representative example of a duplex forming oligonucleotide sequence. FIG. 14C shows a non-limiting example of the self assembly schematic of a representative duplex forming oligonucleotide sequence. FIG. 14D shows a non-limiting example of the self assembly schematic of a representative duplex forming oligonucleotide sequence followed by interaction with a target nucleic acid sequence resulting in modulation of gene expression.

FIG. 15 shows a non-limiting example of the design of self complementary DFO constructs utilizing palidrome and/or repeat nucleic acid sequences that are incorporated into the DFO constructs that have sequence complementary to any target nucleic acid sequence of interest. Incorporation of these palindrome/repeat sequences allow the design of DFO constructs that form duplexes in which each strand is capable of mediating modulation of target gene expression, for example by RNAi. First, the target sequence is identified. A complementary sequence is then generated in which nucleotide or non-nucleotide modifications (shown as X or Y) are introduced into the complementary sequence that generate an artificial palindrome (shown as XYXYXY in the Figure). An inverse repeat of the non-palindrome/repeat complementary sequence is appended to the 3′-end of the complementary sequence to generate a self complementary DFO comprising sequence complementary to the nucleic acid target. The DFO can self-assemble to form a double stranded oligonucleotide.

FIG. 16 shows non-limiting examples of multifunctional siNA molecules of the invention comprising two separate polynucleotide sequences that are each capable of mediating RNAi directed cleavage of differing target nucleic acid sequences. FIG. 16A shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first and second complementary regions are situated at the 3′-ends of each polynucleotide sequence in the multifunctional siNA. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. FIG. 16B shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first and second complementary regions are situated at the 5′-ends of each polynucleotide sequence in the multifunctional siNA. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences.

FIG. 17 shows non-limiting examples of multifunctional siNA molecules of the invention comprising a single polynucleotide sequence comprising distinct regions that are each capable of mediating RNAi directed cleavage of differing target nucleic acid sequences. FIG. 17A shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the second complementary region is situated at the 3′-end of the polynucleotide sequence in the multifunctional siNA. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. FIG. 17B shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first complementary region is situated at the 5′-end of the polynucleotide sequence in the multifunctional siNA. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. In one embodiment, these multifunctional siNA constructs are processed in vivo or in vitro to generate multifunctional siNA constructs as shown in FIG. 16.

FIG. 18 shows non-limiting examples of multifunctional siNA molecules of the invention comprising two separate polynucleotide sequences that are each capable of mediating RNAi directed cleavage of differing target nucleic acid sequences and wherein the multifunctional siNA construct further comprises a self complementary, palindrome, or repeat region, thus enabling shorter bifuctional siNA constructs that can mediate RNA interference against differing target nucleic acid sequences. FIG. 18A shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first and second complementary regions are situated at the 3′-ends of each polynucleotide sequence in the multifunctional siNA, and wherein the first and second complementary regions further comprise a self complementary, palindrome, or repeat region. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. FIG. 18B shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first and second complementary regions are situated at the 5′-ends of each polynucleotide sequence in the multifunctional siNA, and wherein the first and second complementary regions further comprise a self complementary, palindrome, or repeat region. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences.

FIG. 19 shows non-limiting examples of multifunctional siNA molecules of the invention comprising a single polynucleotide sequence comprising distinct regions that are each capable of mediating RNAi directed cleavage of differing target nucleic acid sequences and wherein the multifunctional siNA construct further comprises a self complementary, palindrome, or repeat region, thus enabling shorter bifuctional siNA constructs that can mediate RNA interference against differing target nucleic acid sequences. FIG. 19A shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the second complementary region is situated at the 3′-end of the polynucleotide sequence in the multifunctional siNA, and wherein the first and second complementary regions further comprise a self complementary, palindrome, or repeat region. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. FIG. 19B shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first complementary region is situated at the 5′-end of the polynucleotide sequence in the multifunctional siNA, and wherein the first and second complementary regions further comprise a self complementary, palindrome, or repeat region. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. In one embodiment, these multifunctional siNA constructs are processed in vivo or in vitro to generate multifunctional siNA constructs as shown in FIG. 18.

FIG. 20 shows a non-limiting example of how multifunctional siNA molecules of the invention can target two separate target nucleic acid molecules, such as separate RNA molecules encoding differing proteins, for example, a cytokine and its corresponding receptor, differing viral strains, a virus and a cellular protein involved in viral infection or replication, or differing proteins involved in a common or divergent biologic pathway that is implicated in the maintenance of progression of disease. Each strand of the multifunctional siNA construct comprises a region having complementarity to separate target nucleic acid molecules. The multifunctional siNA molecule is designed such that each strand of the siNA can be utilized by the RISC complex to initiate RNA interference mediated cleavage of its corresponding target. These design parameters can include destabilization of each end of the siNA construct (see for example Schwarz et al., 2003, Cell, 115, 199-208). Such destabilization can be accomplished for example by using guanosine-cytidine base pairs, alternate base pairs (e.g., wobbles), or destabilizing chemically modified nucleotides at terminal nucleotide positions as is known in the art.

FIG. 21 shows a non-limiting example of how multifunctional siNA molecules of the invention can target two separate target nucleic acid sequences within the same target nucleic acid molecule, such as alternate coding regions of a RNA, coding and non-coding regions of a RNA, or alternate splice variant regions of a RNA. Each strand of the multifunctional siNA construct comprises a region having complementarity to the separate regions of the target nucleic acid molecule. The multifunctional siNA molecule is designed such that each strand of the siNA can be utilized by the RISC complex to initiate RNA interference mediated cleavage of its corresponding target region. These design parameters can include destabilization of each end of the siNA construct (see for example Schwarz et al., 2003, Cell, 115, 199-208). Such destabilization can be accomplished for example by using guanosine-cytidine base pairs, alternate base pairs (e.g., wobbles), or destabilizing chemically modified nucleotides at terminal nucleotide positions as is known in the art.

FIG. 22 shows a non-limiting example of reduction of BACE mRNA levels in A549 cells after treatment with siNA molecules targeting BACE mRNA. A549 cells were transfected with 0.25 ug/well of lipid complexed with 25 nM siNA. A screen of siNA constructs comprising ribonucleotides and 3′-terminal dithymidine caps was compared to untreated cells, scrambled siNA control constructs (Scram 1 and Scram 2), and the cells transfected with lipid alone (transfection control). As shown in the Figure, all of the siNA constructs show significant reduction of BACE RNA expression.

FIG. 23 shows a non-limiting example of reduction of BACE mRNA levels in A549 cells (5,000 cells/well) 24 hours after treatment with siNA molecules targeting BACE mRNA. A549 cells were transfected with 0.25 ug/well of lipid complexed with 25 nM siNA. A lead siNA construct (31007/31083) chosen from the screen described in FIG. 22 was further modified using chemical modifications described in Table IV herein. Chemically modified constructs having Stab 4/5 chemistry (31378/31381) and Stab 7/11 chemistry (31384/31387) (solid bars; see Tables m and IV) were tested for efficacy compared to matched chemistry inverted controls (open bars; sequences shown in Table III). The original lead siNA construct (31007/31083) and the Stab 4/5 and Stab 7/11 constructs were compared to untreated cells, scrambled siNA control constructs (Scram1 and Scram2), and cells transfected with lipid alone (transfection control). As shown in the figure, the original lead construct and the Stab 4/5 and Stab 7/11 modified siNA constructs all show significant reduction of BACE RNA expression.

FIG. 24 shows a non-limiting example of reduction of APP mRNA in SK—N—SH cells mediated by chemically modified siNAs that target APP mRNA. SK—N—SH cells were transfected with 0.25 ug/well of lipid complexed with 25 nM siNA. Active siNA constructs comprising various stabilization chemistries (solid bars; see Tables m and IV) were compared to untreated cells, matched chemistry irrelevant siNA control constructs (IC1), and cells transfected with lipid alone (transfection control). As shown in the figure, the siNA constructs significantly reduce APP RNA expression.

FIG. 25 shows a non-limiting example of reduction of PSEN1 mRNA in SK—N—SH cells mediated by chemically modified siNAs that target PSEN1 mRNA. SK—N—SH cells were transfected with 0.25 ug/well of lipid complexed with 25 nM siNA. Active siNA constructs comprising various stabilization chemistries (solid bars; see Tables III and IV) were compared to untreated cells, matched chemistry irrelevant siNA control constructs (IC1), and cells transfected with lipid alone (transfection control). As shown in the figure, the siNA constructs significantly reduce PSEN1 RNA expression.

FIG. 26 shows a non-limiting example of reduction of PSEN2 mRNA in SK—N—SH cells mediated by chemically modified siNAs that target PSEN2 mRNA. SK—N—SH cells were transfected with 0.25 ug/well of lipid complexed with 25 nM siNA. Active siNA constructs comprising various stabilization chemistries (solid bars; see Tables III and IV) were compared to untreated cells, matched chemistry irrelevant siNA control constructs (IC1), and cells transfected with lipid alone (transfection control). As shown in the figure, the siNA constructs significantly reduce PSEN2 RNA expression.

DETAILED DESCRIPTION OF THE INVENTION

Mechanism of Action of Nucleic Acid Molecules of the Invention

The discussion that follows discusses the proposed mechanism of RNA interference mediated by short interfering RNA as is presently known, and is not meant to be limiting and is not an admission of prior art. Applicant demonstrates herein that chemically-modified short interfering nucleic acids possess similar or improved capacity to mediate RNAi as do siRNA molecules and are expected to possess improved stability and activity in vivo; therefore, this discussion is not meant to be limiting only to siRNA and can be applied to siNA as a whole. By “improved capacity to mediate RNAi” or “improved RNAi activity” is meant to include RNAi activity measured in vitro and/or in vivo where the RNAi activity is a reflection of both the ability of the siNA to mediate RNAi and the stability of the siNAs of the invention. In this invention, the product of these activities can be increased in vitro and/or in vivo compared to an all RNA siRNA or a siNA containing a plurality of ribonucleotides. In some cases, the activity or stability of the siNA molecule can be decreased (i.e., less than ten-fold), but the overall activity of the siNA molecule is enhanced in vitro and/or in vivo.

RNA interference refers to the process of sequence specific post-transcriptional gene silencing in animals mediated by short interfering RNAs (siRNAs) (Fire et al., 1998, Nature, 391, 806). The corresponding process in plants is commonly referred to as post-transcriptional gene silencing or RNA silencing and is also referred to as quelling in fungi. The process of post-transcriptional gene silencing is thought to be an evolutionarily-conserved cellular defense mechanism used to prevent the expression of foreign genes which is commonly shared by diverse flora and phyla (Fire et al., 1999, Trends Genet., 15, 358). Such protection from foreign gene expression may have evolved in response to the production of double-stranded RNAs (dsRNAs) derived from viral infection or the random integration of transposon elements into a host genome via a cellular response that specifically destroys homologous single-stranded RNA or viral genomic RNA. The presence of dsRNA in cells triggers the RNAi response though a mechanism that has yet to be fully characterized. This mechanism appears to be different from the interferon response that results from dsRNA-mediated activation of protein kinase PKR and 2′,5′-oligoadenylate synthetase resulting in non-specific cleavage of mRNA by ribonuclease L.

The presence of long dsRNAs in cells stimulates the activity of a ribonuclease III enzyme referred to as Dicer. Dicer is involved in the processing of the dsRNA into short pieces of dsRNA known as short interfering RNAs (siRNAs) (Berstein et al., 2001, Nature, 409, 363). Short interfering RNAs derived from Dicer activity are typically about 21 to about 23 nucleotides in length and comprise about 19 base pair duplexes. Dicer has also been implicated in the excision of 21- and 22-nucleotide small temporal RNAs (stRNAs) from precursor RNA of conserved structure that are implicated in translational control (Hutvagner et al., 2001, Science, 293, 834). The RNAi response also features an endonuclease complex containing a siRNA, commonly referred to as an RNA-induced silencing complex (RISC), which mediates cleavage of single-stranded RNA having sequence homologous to the siRNA. Cleavage of the target RNA takes place in the middle of the region complementary to the guide sequence of the siRNA duplex (Elbashir et al., 2001, Genes Dev., 15, 188). In addition, RNA interference can also involve small RNA (e.g., micro-RNA or mRNA) mediated gene silencing, presumably though cellular mechanisms that regulate chromatin structure and thereby prevent transcription of target gene sequences (see for example Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237). As such, siNA molecules of the invention can be used to mediate gene silencing via interaction with RNA transcripts or alternately by interaction with particular gene sequences, wherein such interaction results in gene silencing either at the transcriptional level or post-transcriptional level.

RNAi has been studied in a variety of systems. Fire et al., 1998, Nature, 391, 806, were the first to observe RNAi in C. elegans. Wianny and Goetz, 1999, Nature Cell Biol., 2, 70, describe RNAi mediated by dsRNA in mouse embryos. Hammond et al., 2000, Nature, 404, 293, describe RNAi in Drosophila cells transfected with dsRNA. Elbashir et al., 2001, Nature, 411, 494, describe RNAi induced by introduction of duplexes of synthetic 21-nucleotide RNAs in cultured mammalian cells including human embryonic kidney and HeLa cells. Recent work in Drosophila embryonic lysates has revealed certain requirements for siRNA length, structure, chemical composition, and sequence that are essential to mediate efficient RNAi activity. These studies have shown that 21 nucleotide siRNA duplexes are most active when containing two 2-nucleotide 3′-terminal nucleotide overhangs. Furthermore, substitution of one or both siRNA strands with 2′-deoxy or 2′-O-methyl nucleotides abolishes RNAi activity, whereas substitution of 3′-terminal siRNA nucleotides with deoxy nucleotides was shown to be tolerated. Mismatch sequences in the center of the siRNA duplex were also shown to abolish RNAi activity. In addition, these studies also indicate that the position of the cleavage site in the target RNA is defined by the 5′-end of the siRNA guide sequence rather than the 3′-end (Elbashir et al., 2001, EMBO J., 20, 6877). Other studies have indicated that a 5′-phosphate on the target-complementary strand of a siRNA duplex is required for siRNA activity and that ATP is utilized to maintain the 5′-phosphate moiety on the siRNA (Nykanen et al., 2001, Cell, 107, 309); however, siRNA molecules lacking a 5′-phosphate are active when introduced exogenously, suggesting that 5′-phosphorylation of siRNA constructs may occur in vivo.

Synthesis of Nucleic Acid Molecules

Synthesis of nucleic acids greater than 100 nucleotides in length is difficult using automated methods, and the therapeutic cost of such molecules is prohibitive. In this invention, small nucleic acid motifs (“small” refers to nucleic acid motifs no more than 100 nucleotides in length, preferably no more than 80 nucleotides in length, and most preferably no more than 50 nucleotides in length; e.g., individual siNA oligonucleotide sequences or siNA sequences synthesized in tandem) are preferably used for exogenous delivery. The simple structure of these molecules increases the ability of the nucleic acid to invade targeted regions of protein and/or RNA structure. Exemplary molecules of the instant invention are chemically synthesized, and others can similarly be synthesized.

Oligonucleotides (e.g., certain modified oligonucleotides or portions of oligonucleotides lacking ribonucleotides) are synthesized using protocols known in the art, for example as described in Caruthers et al., 1992, Methods in Enzymology 211, 3-19, Thompson et al., International PCT Publication No. WO 99/54459, Wincott et al., 1995, Nucleic Acids Res. 23, 2677-2684, Wincott et al., 1997, Methods Mol. Bio., 74, 59, Brennan et al., 1998, Biotechnol Bioeng., 61, 33-45, and Brennan, U.S. Pat. No. 6,001,311. All of these references are incorporated herein by reference. The synthesis of oligonucleotides makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5′-end, and phosphoramidites at the 3′-end. In a non-limiting example, small scale syntheses are conducted on a 394 Applied Biosystems, Inc. synthesizer using a 0.2 μmol scale protocol with a 2.5 min coupling step for 2′-O-methylated nucleotides and a 45 second coupling step for 2′-deoxy nucleotides or 2′-deoxy-2′-fluoro nucleotides. Table V outlines the amounts and the contact times of the reagents used in the synthesis cycle. Alternatively, syntheses at the 0.2 μmol scale can be performed on a 96-well plate synthesizer, such as the instrument produced by Protogene (Palo Alto, Calif.) with minimal modification to the cycle. A 33-fold excess (60 μL of 0.11 M=6.6 μmol) of 2′-O-methyl phosphoramidite and a 105-fold excess of S-ethyl tetrazole (60 μL of 0.25 M=15 μmol) can be used in each coupling cycle of 2′-O-methyl residues relative to polymer-bound 5′-hydroxyl. A 22-fold excess (40 μL of 0.11 M=4.4 μmol) of deoxy phosphoramidite and a 70-fold excess of S-ethyl tetrazole (40 μL of 0.25 M=10 μmol) can be used in each coupling cycle of deoxy residues relative to polymer-bound 5′-hydroxyl. Average coupling yields on the 394 Applied Biosystems, Inc. synthesizer, determined by colorimetric quantitation of the trityl fractions, are typically 97.5-99%. Other oligonucleotide synthesis reagents for the 394 Applied Biosystems, Inc. synthesizer include the following: detritylation solution is 3% TCA in methylene chloride (ABI); capping is performed with 16% N-methyl imidazole in THF (ABI) and 10% acetic anhydride/10% 2,6-lutidine in THF (ABI); and oxidation solution is 16.9 mM I₂, 49 mM pyridine, 9% water in THF (PerSeptive Biosystems, Inc.). Burdick & Jackson Synthesis Grade acetonitrile is used directly from the reagent bottle. S-Ethyltetrazole solution (0.25 M in acetonitrile) is made up from the solid obtained from American International Chemical, Inc. Alternately, for the introduction of phosphorothioate linkages, Beaucage reagent (3H-1,2-Benzodithiol-3-one 1,1-dioxide, 0.05 M in acetonitrile) is used.

Deprotection of the DNA-based oligonucleotides is performed as follows: the polymer-bound trityl-on oligoribonucleotide is transferred to a 4 mL glass screw top vial and suspended in a solution of 40% aqueous methylamine (1 mL) at 65° C. for 10 minutes. After cooling to −20° C., the supernatant is removed from the polymer support. The support is washed three times with 1.0 mL of EtOH:MeCN:H₂O/3:1:1, vortexed and the supernatant is then added to the first supernatant. The combined supernatants, containing the oligoribonucleotide, are dried to a white powder.

The method of synthesis used for RNA including certain siNA molecules of the invention follows the procedure as described in Usman et al., 1987, J. Am. Chem. Soc., 109, 7845; Scaringe et al., 1990, Nucleic Acids Res., 18, 5433; and Wincott et al., 1995, Nucleic Acids Res. 23, 2677-2684 Wincott et al., 1997, Methods Mol. Bio., 74, 59, and makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5′-end, and phosphoramidites at the 3′-end. In a non-limiting example, small scale syntheses are conducted on a 394 Applied Biosystems, Inc. synthesizer using a 0.2 μmol scale protocol with a 7.5 min coupling step for alkylsilyl protected nucleotides and a 2.5 min coupling step for 2′-O-methylated nucleotides. Table V outlines the amounts and the contact times of the reagents used in the synthesis cycle. Alternatively, syntheses at the 0.2 μmol scale can be done on a 96-well plate synthesizer, such as the instrument produced by Protogene (Palo Alto, Calif.) with minimal modification to the cycle. A 33-fold excess (60 μL of 0.11 M=6.6 μmol) of 2′-O-methyl phosphoramidite and a 75-fold excess of S-ethyl tetrazole (60 μL of 0.25 M=15 μmol) can be used in each coupling cycle of 2′-O-methyl residues relative to polymer-bound 5′-hydroxyl. A 66-fold excess (120 μL of 0.11 M=13.2 μmol) of alkylsilyl (ribo) protected phosphoramidite and a 150-fold excess of S-ethyl tetrazole (120 μL of 0.25 M=30 μmol) can be used in each coupling cycle of ribo residues relative to polymer-bound 5′-hydroxyl. Average coupling yields on the 394 Applied Biosystems, Inc. synthesizer, determined by colorimetric quantitation of the trityl fractions, are typically 97.5-99%. Other oligonucleotide synthesis reagents for the 394 Applied Biosystems, Inc. synthesizer include the following: detritylation solution is 3% TCA in methylene chloride (ABI); capping is performed with 16% N-methyl imidazole in THF (ABI) and 10% acetic anhydride/10% 2,6-lutidine in THF (ABI); oxidation solution is 16.9 mM I₂, 49 mM pyridine, 9% water in THF (PerSeptive Biosystems, Inc.). Burdick & Jackson Synthesis Grade acetonitrile is used directly from the reagent bottle. S-Ethyltetrazole solution (0.25 M in acetonitrile) is made up from the solid obtained from American International Chemical, Inc. Alternately, for the introduction of phosphorothioate linkages, Beaucage reagent (3H-1,2-Benzodithiol-3-one 1,1-dioxide0.05 M in acetonitrile) is used.

Deprotection of the RNA is performed using either a two-pot or one-pot protocol. For the two-pot protocol, the polymer-bound trityl-on oligoribonucleotide is transferred to a 4 mL glass screw top vial and suspended in a solution of 40% aq. methylamine (1 mL) at 65° C. for 10 min. After cooling to −20° C., the supernatant is removed from the polymer support. The support is washed three times with 1.0 mL of EtOH:MeCN:H₂O/3:1:1, vortexed and the supernatant is then added to the first supernatant. The combined supernatants, containing the oligoribonucleotide, are dried to a white powder. The base deprotected oligoribonucleotide is resuspended in anhydrous TEA/HF/NMP solution (300 μL of a solution of 1.5 mL N-methylpyrrolidinone, 750 μL TEA and 1 mL TEA·3BF to provide a 1.4 M HF concentration) and heated to 65° C. After 1.5 h, the oligomer is quenched with 1.5 M NH₄HCO₃.

Alternatively, for the one-pot protocol, the polymer-bound trityl-on oligoribonucleotide is transferred to a 4 mL glass screw top vial and suspended in a solution of 33% ethanolic methylamine/DMSO: 1/1 (0.8 mL) at 65° C. for 15 minutes. The vial is brought to room temperature TEA-3HF (0.1 mL) is added and the vial is heated at 65° C. for 15 minutes. The sample is cooled at −20° C. and then quenched with 1.5 M NH₄HCO₃.

For purification of the trityl-on oligomers, the quenched NH₄HCO₃ solution is loaded onto a C-18 containing cartridge that had been prewashed with acetonitrile followed by 50 mM TEAA. After washing the loaded cartridge with water, the RNA is detritylated with 0.5% TFA for 13 minutes. The cartridge is then washed again with water, salt exchanged with 1 M NaCl and washed with water again. The oligonucleotide is then eluted with 30% acetonitrile.

The average stepwise coupling yields are typically >98% (Wincott et al., 1995 Nucleic Acids Res. 23, 2677-2684). Those of ordinary skill in the art will recognize that the scale of synthesis can be adapted to be larger or smaller than the example described above including but not limited to 96-well format.

Alternatively, the nucleic acid molecules of the present invention can be synthesized separately and joined together post-synthetically, for example, by ligation (Moore et al., 1992, Science 256, 9923; Draper et al., International PCT publication No. WO 93/23569; Shabarova et al., 1991, Nucleic Acids Research 19, 4247; Bellon et al, 1997, Nucleosides & Nucleotides, 16, 951; Bellon et al., 1997, Bioconjugate Chem. 8, 204), or by hybridization following synthesis and/or deprotection.

The siNA molecules of the invention can also be synthesized via a tandem synthesis methodology as described in Example 1 herein, wherein both siNA strands are synthesized as a single contiguous oligonucleotide fragment or strand separated by a cleavable linker which is subsequently cleaved to provide separate siNA fragments or strands that hybridize and permit purification of the siNA duplex. The linker can be a polynucleotide linker or a non-nucleotide linker. The tandem synthesis of siNA as described herein can be readily adapted to both multiwell/multiplate synthesis platforms such as 96 well or similarly larger multi-well platforms. The tandem synthesis of siNA as described herein can also be readily adapted to large scale synthesis platforms employing batch reactors, synthesis columns and the like.

A siNA molecule can also be assembled from two distinct nucleic acid strands or fragments wherein one fragment includes the sense region and the second fragment includes the antisense region of the RNA molecule.

The nucleic acid molecules of the present invention can be modified extensively to enhance stability by modification with nuclease resistant groups, for example, 2′-amino, 2′-C-allyl, 2′-fluoro, 2′-O-methyl, 2′-H (for a review see Usman and Cedergren, 1992, TIBS 17, 34; Usman et al., 1994, Nucleic Acids Symp. Ser. 31, 163). siNA constructs can be purified by gel electrophoresis using general methods or can be purified by high pressure liquid chromatography (HPLC; see Wincott et al., supra, the totality of which is hereby incorporated herein by reference) and re-suspended in water.

In another aspect of the invention, siNA molecules of the invention are expressed from transcription units inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. siNA expressing viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. The recombinant vectors capable of expressing the siNA molecules can be delivered as described herein, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of siNA molecules.

Optimizing Activity of the Nucleic Acid Molecule of the Invention.

Chemically synthesizing nucleic acid molecules with modifications (base, sugar and/or phosphate) can prevent their degradation by serum ribonucleases, which can increase their potency (see e.g., Eckstein et al., International Publication No. WO 92/07065; Perrault et al., 1990 Nature 344, 565; Pieken et al., 1991, Science 253, 314; Usman and Cedergren, 1992, Trends in Biochem. Sci. 17, 334; Usman et al., International Publication No. WO 93/15187; and Rossi et al., International Publication No. WO 91/03162; Sproat, U.S. Pat. No. 5,334,711; Gold et al., U.S. Pat. No. 6,300,074; and Burgin et al., supra; all of which are incorporated by reference herein). All of the above references describe various chemical modifications that can be made to the base, phosphate and/or sugar moieties of the nucleic acid molecules described herein. Modifications that enhance their efficacy in cells, and removal of bases from nucleic acid molecules to shorten oligonucleotide synthesis times and reduce chemical requirements are desired.

There are several examples in the art describing sugar, base and phosphate modifications that can be introduced into nucleic acid molecules with significant enhancement in their nuclease stability and efficacy. For example, oligonucleotides are modified to enhance stability and/or enhance biological activity by modification with nuclease resistant groups, for example, 2′-amino, 2′-C-allyl, 2′-fluoro, 2′-O-methyl, 2′-O-allyl, 2′-H, nucleotide base modifications (for a review see Usman and Cedergren, 1992, TIBS. 17, 34; Usman et al., 1994, Nucleic Acids Symp. Ser. 31, 163; Burgin et al., 1996, Biochemistry, 35, 14090). Sugar modification of nucleic acid molecules have been extensively described in the art (see Eckstein et al., International Publication PCT No. WO 92/07065; Perrault et al. Nature, 1990, 344, 565-568; Pieken et al. Science, 1991, 253, 314-317; Usman and Cedergren, Trends in Biochem. Sci., 1992, 17, 334-339; Usman et al. International Publication PCT No. WO 93/15187; Sproat, U.S. Pat. No. 5,334,711 and Beigelman et al., 1995, J. Biol. Chem., 270, 25702; Beigelman et al., International PCT publication No. WO 97/26270; Beigelman et al., U.S. Pat. No. 5,716,824; Usman et al., U.S. Pat. No. 5,627,053; Woolf et al., International PCT Publication No. WO 98/13526; Thompson et al., U.S. Ser. No. 60/082,404 which was filed on Apr. 20, 1998; Karpeisky et al., 1998, Tetrahedron Lett., 39, 1131; Earnshaw and Gait, 1998, Biopolymers (Nucleic Acid Sciences), 48, 39-55; Verma and Eckstein, 1998, Annu. Rev. Biochem., 67, 99-134; and Burlina et al. 1997, Bioorg. Med. Chem., 5, 1999-2010; all of the references are hereby incorporated in their totality by reference herein). Such publications describe general methods and strategies to determine the location of incorporation of sugar, base and/or phosphate modifications and the like into nucleic acid molecules without modulating catalysis, and are incorporated by reference herein. In view of such teachings, similar modifications can be used as described herein to modify the siNA nucleic acid molecules of the instant invention so long as the ability of siNA to promote RNAi is cells is not significantly inhibited.

While chemical modification of oligonucleotide internucleotide linkages with phosphorothioate, phosphorodithioate, and/or 5′-methylphosphonate linkages improves stability, excessive modifications can cause some toxicity or decreased activity. Therefore, when designing nucleic acid molecules, the amount of these internucleotide linkages should be minimized. The reduction in the concentration of these linkages should lower toxicity, resulting in increased efficacy and higher specificity of these molecules.

Short interfering nucleic acid (siNA) molecules having chemical modifications that maintain or enhance activity are provided. Such a nucleic acid is also generally more resistant to nucleases than an unmodified nucleic acid. Accordingly, the in vitro and/or in vivo activity should not be significantly lowered. In cases in which modulation is the goal, therapeutic nucleic acid molecules delivered exogenously should optimally be stable within cells until translation of the target RNA has been modulated long enough to reduce the levels of the undesirable protein. This period of time varies between hours to days depending upon the disease state. Improvements in the chemical synthesis of RNA and DNA (Wincott et al., 1995, Nucleic Acids Res. 23, 2677; Caruthers et al., 1992, Methods in Enzymology 211, 3-19 (incorporated by reference herein)) have expanded the ability to modify nucleic acid molecules by introducing nucleotide modifications to enhance their nuclease stability, as described above.

In one embodiment, nucleic acid molecules of the invention include one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) G-clamp nucleotides. A G-clamp nucleotide is a modified cytosine analog wherein the modifications confer the ability to hydrogen bond both Watson-Crick and Hoogsteen faces of a complementary guanine within a duplex, see for example Lin and Matteucci, 1998, J. Am. Chem. Soc., 120, 8531-8532. A single G-clamp analog substitution within an oligonucleotide can result in substantially enhanced helical thermal stability and mismatch discrimination when hybridized to complementary oligonucleotides. The inclusion of such nucleotides in nucleic acid molecules of the invention results in both enhanced affinity and specificity to nucleic acid targets, complementary sequences, or template strands. In another embodiment, nucleic acid molecules of the invention include one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) LNA “locked nucleic acid” nucleotides such as a 2′,4′-C methylene bicyclo nucleotide (see for example Wengel et al., International PCT Publication No. WO 00/66604 and WO 99/14226).

In another embodiment, the invention features conjugates and/or complexes of siNA molecules of the invention. Such conjugates and/or complexes can be used to facilitate delivery of siNA molecules into a biological system, such as a cell. The conjugates and complexes provided by the instant invention can impart therapeutic activity by transferring therapeutic compounds across cellular membranes, altering the pharmacokinetics, and/or modulating the localization of nucleic acid molecules of the invention. The present invention encompasses the design and synthesis of novel conjugates and complexes for the delivery of molecules, including, but not limited to, small molecules, lipids, cholesterol, phospholipids, nucleosides, nucleotides, nucleic acids, antibodies, toxins, negatively charged polymers and other polymers, for example proteins, peptides, hormones, carbohydrates, polyethylene glycols, or polyamines, across cellular membranes. In general, the transporters described are designed to be used either individually or as part of a multi-component system, with or without degradable linkers. These compounds are expected to improve delivery and/or localization of nucleic acid molecules of the invention into a number of cell types originating from different tissues, in the presence or absence of serum (see Sullenger and Cech, U.S. Pat. No. 5,854,038). Conjugates of the molecules described herein can be attached to biologically active molecules via linkers that are biodegradable, such as biodegradable nucleic acid linker molecules.

The term “biodegradable linker” as used herein, refers to a nucleic acid or non-nucleic acid linker molecule that is designed as a biodegradable linker to connect one molecule to another molecule, for example, a biologically active molecule to a siNA molecule of the invention or the sense and antisense strands of a siNA molecule of the invention. The biodegradable linker is designed such that its stability can be modulated for a particular purpose, such as delivery to a particular tissue or cell type. The stability of a nucleic acid-based biodegradable linker molecule can be modulated by using various chemistries, for example combinations of ribonucleotides, deoxyribonucleotides, and chemically-modified nucleotides, such as 2′-O-methyl, 2′-fluoro, 2′-amino, 2′-O-amino, 2′-C-allyl, 2′-O-allyl, and other 2′-modified or base modified nucleotides. The biodegradable nucleic acid linker molecule can be a dimer, trimer, tetramer or longer nucleic acid molecule, for example, an oligonucleotide of about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides in length, or can comprise a single nucleotide with a phosphorus-based linkage, for example, a phosphoramidate or phosphodiester linkage. The biodegradable nucleic acid linker molecule can also comprise nucleic acid backbone, nucleic acid sugar, or nucleic acid base modifications.

The term “biodegradable” as used herein, refers to degradation in a biological system, for example, enzymatic degradation or chemical degradation.

The term “biologically active molecule” as used herein refers to compounds or molecules that are capable of eliciting or modifying a biological response in a system. Non-limiting examples of biologically active siNA molecules either alone or in combination with other molecules contemplated by the instant invention include therapeutically active molecules such as antibodies, cholesterol, hormones, antivirals, peptides, proteins, chemotherapeutics, small molecules, vitamins, co-factors, nucleosides, nucleotides, oligonucleotides, enzymatic nucleic acids, antisense nucleic acids, triplex forming oligonucleotides, 2,5-A chimeras, siNA, dsRNA, allozymes, aptamers, decoys and analogs thereof. Biologically active molecules of the invention also include molecules capable of modulating the pharmacokinetics and/or pharmacodynamics of other biologically active molecules, for example, lipids and polymers such as polyamines, polyamides, polyethylene glycol and other polyethers.

The term “phospholipid” as used herein, refers to a hydrophobic molecule comprising at least one phosphorus group. For example, a phospholipid can comprise a phosphorus-containing group and saturated or unsaturated alkyl group, optionally substituted with OH, COOH, oxo, amine, or substituted or unsubstituted aryl groups.

Therapeutic nucleic acid molecules (e.g., siNA molecules) delivered exogenously optimally are stable within cells until reverse transcription of the RNA has been modulated long enough to reduce the levels of the RNA transcript. The nucleic acid molecules are resistant to nucleases in order to function as effective intracellular therapeutic agents. Improvements in the chemical synthesis of nucleic acid molecules described in the instant invention and in the art have expanded the ability to modify nucleic acid molecules by introducing nucleotide modifications to enhance their nuclease stability as described above.

In yet another embodiment, siNA molecules having chemical modifications that maintain or enhance enzymatic activity of proteins involved in RNAi are provided. Such nucleic acids are also generally more resistant to nucleases than unmodified nucleic acids. Thus, in vitro and/or in vivo the activity should not be significantly lowered.

Use of the nucleic acid-based molecules of the invention will lead to better treatments by affording the possibility of combination therapies (e.g., multiple siNA molecules targeted to different genes; nucleic acid molecules coupled with known small molecule modulators; or intermittent treatment with combinations of molecules, including different motifs and/or other chemical or biological molecules). The treatment of subjects with siNA molecules can also include combinations of different types of nucleic acid molecules, such as enzymatic nucleic acid molecules (ribozymes), allozymes, antisense, 2,5-A oligoadenylate, decoys, and aptamers.

In another aspect a siNA molecule of the invention comprises one or more 5′ and/or a 3′-cap structure, for example, on only the sense siNA strand, the antisense siNA strand, or both siNA strands.

By “cap structure” is meant chemical modifications, which have been incorporated at either terminus of the oligonucleotide (see, for example, Adamic et al., U.S. Pat. No. 5,998,203, incorporated by reference herein). These terminal modifications protect the nucleic acid molecule from exonuclease degradation, and may help in delivery and/or localization within a cell. The cap may be present at the 5′-terminus (5′-cap) or at the 3′-terminal (3′-cap) or may be present on both termini. In non-limiting examples, the 5′-cap includes, but is not limited to, glyceryl, inverted deoxy abasic residue (moiety); 4′,5′-methylene nucleotide; 1-(beta-D-erythrofuranosyl) nucleotide, 4′-thio nucleotide; carbocyclic nucleotide; 1,5-anhydrohexitol nucleotide; L-nucleotides; alpha-nucleotides; modified base nucleotide; phosphorodithioate linkage; threo-pentofuranosyl nucleotide; acyclic 3′,4′-seco nucleotide; acyclic 3,4-dihydroxybutyl nucleotide; acyclic 3,5-dihydroxypentyl nucleotide, 3′-3′-inverted nucleotide moiety; 3′-3′-inverted abasic moiety; 3′-2′-inverted nucleotide moiety; 3′-2′-inverted abasic moiety; 1,4-butanediol phosphate; 3′-phosphoramidate; hexylphosphate; aminohexyl phosphate; 3′-phosphate; 3′-phosphorothioate; phosphorodithioate; or bridging or non-bridging methylphosphonate moiety.

Non-limiting examples of the 3′-cap include, but are not limited to, glyceryl, inverted deoxy abasic residue (moiety), 4′,5′-methylene nucleotide; 1-(beta-D-erythrofuranosyl) nucleotide; 4′-thio nucleotide, carbocyclic nucleotide; 5′-amino-alkyl phosphate; 1,3-diamino-2-propyl phosphate; 3-aminopropyl phosphate; 6-aminohexyl phosphate; 1,2-aminododecyl phosphate; hydroxypropyl phosphate; 1,5-anhydrohexitol nucleotide; L-nucleotide; alpha-nucleotide; modified base nucleotide; phosphorodithioate; threo-pentofuranosyl nucleotide; acyclic 3′,4′-seco nucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentyl nucleotide, 5′-5′-inverted nucleotide moiety; 5′-5′-inverted abasic moiety; 5′-phosphoramidate; 5′-phosphorothioate; 1,4-butanediol phosphate; 5′-amino; bridging and/or non-bridging 5′-phosphoramidate, phosphorothioate and/or phosphorodithioate, bridging or non bridging methylphosphonate and 5′-mercapto moieties (for more details see Beaucage and Iyer, 1993, Tetrahedron 49, 1925; incorporated by reference herein).

By the term “non-nucleotide” is meant any group or compound which can be incorporated into a nucleic acid chain in the place of one or more nucleotide units, including either sugar and/or phosphate substitutions, and allows the remaining bases to exhibit their enzymatic activity. The group or compound is abasic in that it does not contain a commonly recognized nucleotide base, such as adenosine, guanine, cytosine, uracil or thymine and therefore lacks a base at the 1′-position.

An “alkyl” group refers to a saturated aliphatic hydrocarbon, including straight-chain, branched-chain, and cyclic alkyl groups. Preferably, the alkyl group has 1 to 12 carbons. More preferably, it is a lower alkyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The alkyl group can be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, ═O, ═S, NO₂ or N(CH₃)₂, amino, or SH. The term also includes alkenyl groups that are unsaturated hydrocarbon groups containing at least one carbon-carbon double bond, including straight-chain, branched-chain, and cyclic groups. Preferably, the alkenyl group has 1 to 12 carbons. More preferably, it is a lower alkenyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The alkenyl group may be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, ═O, ═S, NO₂, halogen, N(CH₃)₂, amino, or SH. The term “alkyl” also includes alkynyl groups that have an unsaturated hydrocarbon group containing at least one carbon-carbon triple bond, including straight-chain, branched-chain, and cyclic groups. Preferably, the alkynyl group has 1 to 12 carbons. More preferably, it is a lower alkynyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The allynyl group may be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, ═O, ═S, NO₂ or N(CH₃)₂, amino or SH.

Such alkyl groups can also include aryl, alkylaryl, carbocyclic aryl, heterocyclic aryl, amide and ester groups. An “aryl” group refers to an aromatic group that has at least one ring having a conjugated pi electron system and includes carbocyclic aryl, heterocyclic aryl and biaryl groups, all of which may be optionally substituted. The preferred substituent(s) of aryl groups are halogen, trihalomethyl, hydroxyl, SH, OH, cyano, alkoxy, alkyl, alkenyl, alkynyl, and amino groups. An “alkylaryl” group refers to an alkyl group (as described above) covalently joined to an aryl group (as described above). Carbocyclic aryl groups are groups wherein the ring atoms on the aromatic ring are all carbon atoms. The carbon atoms are optionally substituted. Heterocyclic aryl groups are groups having from 1 to 3 heteroatoms as ring atoms in the aromatic ring and the remainder of the ring atoms are carbon atoms. Suitable heteroatoms include oxygen, sulfur, and nitrogen, and include furanyl, thienyl, pyridyl, pyrrolyl, N-lower alkyl pyrrolo, pyrimidyl, pyrazinyl, imidazolyl and the like, all optionally substituted. An “amide” refers to an —C(O)—NH—R, where R is either alkyl, aryl, alkylaryl or hydrogen. An “ester” refers to an —C(O)—OR′, where R is either alkyl, aryl, alkylaryl or hydrogen.

By “nucleotide” as used herein is as recognized in the art to include natural bases (standard), and modified bases well known in the art. Such bases are generally located at the 1′ position of a nucleotide sugar moiety. Nucleotides generally comprise a base, sugar and a phosphate group. The nucleotides can be unmodified or modified at the sugar, phosphate and/or base moiety, (also referred to interchangeably as nucleotide analogs, modified nucleotides, non-natural nucleotides, non-standard nucleotides and other; see, for example, Usman and McSwiggen, supra; Eckstein et al., International PCT Publication No. WO 92/07065; Usman et al., International PCT Publication No. WO 93/15187; Uhlman & Peyman, supra, all are hereby incorporated by reference herein). There are several examples of modified nucleic acid bases known in the art as summarized by Limbach et al., 1994, Nucleic Acids Res. 22, 2183. Some of the non-limiting examples of base modifications that can be introduced into nucleic acid molecules include, inosine, purine, pyridin-4-one, pyridin-2-one, phenyl, pseudouracil, 2, 4, 6-trimethoxy benzene, 3-methyl uracil, dihydrouridine, naphthyl, aminophenyl, 5-alkylcytidines (e.g., 5-methylcytidine), 5-alkyluridines (e.g., ribothymidine), 5-halouridine (e.g., 5-bromouridine) or 6-azapyrimidines or 6-alkylpyrimidines (e.g. 6-methyluridine), propyne, and others (Burgin et al., 1996, Biochemistry, 35, 14090; Uhlman & Peyman, supra). By “modified bases” in this aspect is meant nucleotide bases other than adenine, guanine, cytosine and uracil at 1′ position or their equivalents.

In one embodiment, the invention features modified siNA molecules, with phosphate backbone modifications comprising one or more phosphorothioate, phosphorodithioate, methylphosphonate, phosphotriester, morpholino, amidate carbamate, carboxymethyl, acetamidate, polyamide, sulfonate, sulfonamide, sulfamate, formacetal, thioformacetal, and/or alkylsilyl, substitutions. For a review of oligonucleotide backbone modifications, see Hunziker and Leumann, 1995, Nucleic Acid Analogues: Synthesis and Properties, in Modern Synthetic Methods, VCH, 331-417, and Mesmaeker et al., 1994, Novel Backbone Replacements for Oligonucleotides, in Carbohydrate Modifications in Antisense Research, ACS, 24-39.

By “abasic” is meant sugar moieties lacking a base or having other chemical groups in place of a base at the 1′ position, see for example Adamic et al., U.S. Pat. No. 5,998,203.

By “unmodified nucleoside” is meant one of the bases adenine, cytosine, guanine, thymine, or uracil joined to the 1′ carbon of β-D-ribo-furanose.

By “modified nucleoside” is meant any nucleotide base which contains a modification in the chemical structure of an unmodified nucleotide base, sugar and/or phosphate. Non-limiting examples of modified nucleotides are shown by Formulae I-VII and/or other modifications described herein.

In connection with 2′-modified nucleotides as described for the present invention, by “amino” is meant 2′-NH₂ or 2′-O—NH₂, which can be modified or unmodified. Such modified groups are described, for example, in Eckstein et al., U.S. Pat. No. 5,672,695 and Matulic-Adamic et al., U.S. Pat. No. 6,248,878, which are both incorporated by reference in their entireties.

Various modifications to nucleic acid siNA structure can be made to enhance the utility of these molecules. Such modifications will enhance shelf-life, half-life in vitro, stability, and ease of introduction of such oligonucleotides to the target site, e.g., to enhance penetration of cellular membranes, and confer the ability to recognize and bind to targeted cells.

Administration of Nucleic Acid Molecules

A siNA molecule of the invention can be adapted for use to prevent or treat a variety of neurodegenerative diseases, including Alzheimer's disease, dementia, stroke (CVA), or any other trait, disease or condition that is related to or will respond to the levels of BACE in a cell or tissue, alone or in combination with other therapies.

For example, a siNA molecule can comprise a delivery vehicle, including liposomes, for administration to a subject, carriers and diluents and their salts, and/or can be present in pharmaceutically acceptable formulations. Methods for the delivery of nucleic acid molecules are described in Akhtar et al., 1992, Trends Cell Bio., 2, 139; Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed. Akhtar, 1995, Maurer et al., 1999, Mol. Membr. Biol., 16, 129-140; Hofland and Huang, 1999, Handb. Exp. Pharmacol., 137, 165-192; and Lee et al., 2000, ACS Symp. Ser., 752, 184-192, all of which are incorporated herein by reference. Beigelman et al, U.S. Pat. No. 6,395,713 and Sullivan et al., PCT WO 94/02595 further describe the general methods for delivery of nucleic acid molecules. These protocols can be utilized for the delivery of virtually any nucleic acid molecule. Nucleic acid molecules can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as biodegradable polymers, hydrogels, cyclodextrins (see for example Gonzalez et al., 1999, Bioconjugate Chem., 10, 1068-1074; Wang et al., International PCT publication Nos. WO 03/47518 and WO 03/46185), poly(lactic-co-glycolic)acid (PLGA) and PLCA microspheres (see for example U.S. Pat. No. 6,447,796 and U.S. Patent Application Publication No. US 2002130430), biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors (O'Hare and Normand, International PCT Publication No. WO 00/53722). In another embodiment, the nucleic acid molecules of the invention can also be formulated or complexed with polyethyleneimine and derivatives thereof, such as polyethyleneimine-polyethyleneglycol-N-acetylgalactosamine (PEI-PEG-GAL) or polyethyleneimine-polyethyleneglycol-tri-N-acetylgalactosamine (PEI-PEG-triGAL) derivatives.

In one embodiment, a siNA molecule of the invention is complexed with membrane disruptive agents such as those described in U.S. Patent Application Publication No. 20010007666, incorporated by reference herein in its entirety including the drawings. In another embodiment, the membrane disruptive agent or agents and the siNA molecule are also complexed with a cationic lipid or helper lipid molecule, such as those lipids described in U.S. Pat. No. 6,235,310, incorporated by reference herein in its entirety including the drawings.

In one embodiment, a siNA molecule of the invention is complexed with delivery systems as described in U.S. Patent Application Publication No. 2003077829 and International PCT Publication Nos. WO 00/03683 and WO 02/087541, all incorporated by reference herein in their entirety including the drawings.

In one embodiment, siNA molecules of the invention are formulated or complexed with polyethylenimine (e.g., linear or branched PEI) and/or polyethylenimine derivatives, including for example grafted PEIs such as galactose PEI, cholesterol PEI, antibody derivatized PEI, and polyethylene glycol PEI (PEG-PEI) derivatives thereof (see for example Ogris et al., 2001, AAPA PharmSci, 3, 1-11; Furgeson et al., 2003, Bioconjugate Chem., 14, 840-847; Kunath et al., 2002, Phramaceutical Research, 19, 810-817; Choi et al., 2001, Bull. Korean Chem. Soc., 22, 46-52; Bettinger et al., 1999, Bioconjugate Chem., 10, 558-561; Peterson et al., 2002, Bioconjugate Chem., 13, 845-854; Erbacher et al., 1999, Journal of Gene Medicine Preprint, 1, 1-18; Godbey et al., 1999, PNAS USA, 96, 5177-5181; Godbey et al., 1999, Journal of Controlled Release, 60, 149-160; Diebold et al., 1999, Journal of Biological Chemistry, 274, 19087-19094; Thomas and Klibanov, 2002, PNAS USA, 99, 14640-14645; and Sagara, U.S. Pat. No. 6,586,524, incorporated by reference herein.

In one embodiment, a siNA molecule of the invention comprises a bioconjugate, for example a nucleic acid conjugate as described in Vargeese et al., U.S. Ser. No. 10/427,160, filed Apr. 30, 2003; U.S. Pat. No. 6,528,631; U.S. Pat. No. 6,335,434; U.S. Pat. No. 6,235,886; U.S. Pat. No. 6,153,737; U.S. Pat. No. 5,214,136; U.S. Pat. No. 5,138,045, all incorporated by reference herein.

Thus, the invention features a pharmaceutical composition comprising one or more nucleic acid(s) of the invention in an acceptable carrier, such as a stabilizer, buffer, and the like. The polynucleotides of the invention can be administered (e.g., RNA, DNA or protein) and introduced to a subject by any standard means, with or without stabilizers, buffers, and the like, to form a pharmaceutical composition. When it is desired to use a liposome delivery mechanism, standard protocols for formation of liposomes can be followed. The compositions of the present invention can also be formulated and used as creams, gels, sprays, oils and other suitable compositions for topical, dermal, or transdermal administration as is known in the art.

The present invention also includes pharmaceutically acceptable formulations of the compounds described. These formulations include salts of the above compounds, e.g., acid addition salts, for example, salts of hydrochloric, hydrobromic, acetic acid, and benzene sulfonic acid.

A pharmacological composition or formulation refers to a composition or formulation in a form suitable for administration, e.g., systemic or local administration, into a cell or subject, including for example a human. Suitable forms, in part, depend upon the use or the route of entry, for example oral, transdermal, or by injection. Such forms should not prevent the composition or formulation from reaching a target cell (i.e., a cell to which the negatively charged nucleic acid is desirable for delivery). For example, pharmacological compositions injected into the blood stream should be soluble. Other factors are known in the art, and include considerations such as toxicity and forms that prevent the composition or formulation from exerting its effect.

In one embodiment, the invention features the use of methods to deliver the nucleic acid molecules of the instant invention to the central nervous system and/or peripheral nervous system. Experiments have demonstrated the efficient in vivo uptake of nucleic acids by neurons. As an example of local administration of nucleic acids to nerve cells, Sommer et al., 1998, Antisense Nuc. Acid Drug Dev., 8, 75, describe a study in which a 15mer phosphorothioate antisense nucleic acid molecule to c-fos is administered to rats via microinjection into the brain. Antisense molecules labeled with tetramethylrhodamine-isothiocyanate (TRITC) or fluorescein isothiocyanate (FITC) were taken up by exclusively by neurons thirty minutes post-injection. A diffuse cytoplasmic staining and nuclear staining was observed in these cells. As an example of systemic administration of nucleic acid to nerve cells, Epa et al., 2000, Antisense Nuc. Acid Drug Dev., 10, 469, describe an in vivo mouse study in which beta-cyclodextrin-adamantane-oligonucleotide conjugates were used to target the p75 neurotrophin receptor in neuronally differentiated PC12 cells. Following a two week course of IP administration, pronounced uptake of p75 neurotrophin receptor antisense was observed in dorsal root ganglion (DRG) cells. In addition, a marked and consistent down-regulation of p75 was observed in DRG neurons. Additional approaches to the targeting of nucleic acid to neurons are described in Broaddus et al., 1998, J. Neurosurg., 88(4), 734; Karle et al., 1997, Eur. J. Pharmocol., 340(2/3), 153; Bannai et al., 1998, Brain Research, 784(1,2), 304; Rajakumar et al., 1997, Synapse, 26(3), 199; Wu-pong et al., 1999, BioPharm, 12(1), 32; Bannai et al., 1998, Brain Res. Protoc., 3(1), 83; Simantov et al., 1996, Neuroscience, 74(1), 39. Nucleic acid molecules of the invention are therefore amenable to delivery to and uptake by cells that express repeat expansion allelic variants for modulation of RE gene expression. The delivery of nucleic acid molecules of the invention, targeting RE is provided by a variety of different strategies. Traditional approaches to CNS delivery that can be used include, but are not limited to, intrathecal and intracerebroventricular administration, implantation of catheters and pumps, direct injection or perfusion at the site of injury or lesion, injection into the brain arterial system, or by chemical or osmotic opening of the blood-brain barrier. Other approaches can include the use of various transport and carrier systems, for example though the use of conjugates and biodegradable polymers. Furthermore, gene therapy approaches, for example as described in Kaplitt et al., U.S. Pat. No. 6,180,613 and Davidson, WO 04/013280, can be used to express nucleic acid molecules in the CNS.

In one embodiment, nucleic acid molecules of the invention are administered to the central nervous system (CNS) or peripheral nervous system (PNS). Experiments have demonstrated the efficient in vivo uptake of nucleic acids by neurons. As an example of local administration of nucleic acids to nerve cells, Sommer et al., 1998, Antisense Nuc. Acid Drug Dev., 8, 75, describe a study in which a 15mer phosphorothioate antisense nucleic acid molecule to c-fos is administered to rats via microinjection into the brain. Antisense molecules labeled with tetramethylrhodamine-isothiocyanate (TRITC) or fluorescein isothiocyanate (FITC) were taken up by exclusively by neurons thirty minutes post-injection. A diffuse cytoplasmic staining and nuclear staining was observed in these cells. As an example of systemic administration of nucleic acid to nerve cells, Epa et al., 2000, Antisense Nuc. Acid Drug Dev., 10, 469, describe an in vivo mouse study in which beta-cyclodextrin-adamantane-oligonucleotide conjugates were used to target the p75 neurotrophin receptor in neuronally differentiated PC12 cells. Following a two week course of IP administration, pronounced uptake of p75 neurotrophin receptor antisense was observed in dorsal root ganglion (DRG) cells. In addition, a marked and consistent down-regulation of p75 was observed in DRG neurons. Additional approaches to the targeting of nucleic acid to neurons are described in Broaddus et al., 1998, J. Neurosurg., 88(4), 734; Karle et al., 1997, Eur. J. Pharmocol., 340(2/3), 153; Bannai et al., 1998, Brain Research, 784(1,2), 304; Rajakumar et al., 1997, Synapse, 26(3), 199; Wu-pong et al., 1999, BioPharm, 12(1), 32; Bannai et al., 1998, Brain Res. Protoc., 3(1), 83; Simantov et al., 1996, Neuroscience, 74(1), 39. Nucleic acid molecules of the invention are therefore amenable to delivery to and uptake by cells in the CNS and/or PNS.

The delivery of nucleic acid molecules of the invention to the CNS is provided by a variety of different strategies. Traditional approaches to CNS delivery that can be used include, but are not limited to, intrathecal and intracerebroventricular administration, implantation of catheters and pumps, direct injection or perfusion at the site of injury or lesion, injection into the brain arterial system, or by chemical or osmotic opening of the blood-brain barrier. Other approaches can include the use of various transport and carrier systems, for example though the use of conjugates and biodegradable polymers. Furthermore, gene therapy approaches, for example as described in Kaplitt et al., U.S. Pat. No. 6,180,613 and Davidson, WO 04/013280, can be used to express nucleic acid molecules in the CNS.

In one embodiment, dermal delivery systems of the invention include, for example, aqueous and nonaqueous gels, creams, multiple emulsions, microemulsions, liposomes, ointments, aqueous and nonaqueous solutions, lotions, aerosols, hydrocarbon bases and powders, and can contain excipients such as solubilizers, permeation enhancers (e.g., fatty acids, fatty acid esters, fatty alcohols and amino acids), and hydrophilic polymers (e.g., polycarbophil and polyvinylpyrolidone). In one embodiment, the pharmaceutically acceptable carrier is a liposome or a transdermal enhancer. Examples of liposomes which can be used in this invention include the following: (1) CellFectin, 1:1.5 (M/M) liposome formulation of the cationic lipid N,NII,NIII-tetramethyl-N,NI,NII,NIII-tetrapalmit-y-spermine and dioleoyl phosphatidylethanolamine (DOPE) (GIBCO BRL); (2) Cytofectin GSV, 2:1 (M/M) liposome formulation of a cationic lipid and DOPE (Glen Research); (3) DOTAP (N-[1-(2,3-dioleoyloxy)-N,N,N-tri-methyl-ammoniummethylsulfate) (Boehringer Manheim); and (4) Lipofectamine, 3:1 (M/M) liposome formulation of the polycationic lipid DOSPA and the neutral lipid DOPE (GIBCO BRL).

In one embodiment, siNA molecules of the invention are administered to a subject by systemic administration in a pharmaceutically acceptable composition or formulation. By “systemic administration” is meant in vivo systemic absorption or accumulation of drugs in the blood stream followed by distribution throughout the entire body. Administration routes that lead to systemic absorption include, without limitation: intravenous, subcutaneous, intraperitoneal, inhalation, oral, intrapulmonary and intramuscular. Each of these administration routes exposes the siNA molecules of the invention to an accessible diseased tissue. The rate of entry of a drug into the circulation has been shown to be a function of molecular weight or size. The use of a liposome or other drug carrier comprising the compounds of the instant invention can potentially localize the drug, for example, in certain tissue types, such as the tissues of the reticular endothelial system (RES). A liposome formulation that can facilitate the association of drug with the surface of cells, such as, lymphocytes and macrophages is also useful. This approach can provide enhanced delivery of the drug to target cells by taking advantage of the specificity of macrophage and lymphocyte immune recognition of abnormal cells.

In one embodiment, siNA molecules of the invention are formulated or complexed with polyethylenimine (e.g., linear or branched PEI) and/or polyethylenimine derivatives, including for example grafted PEIs such as galactose PEI, cholesterol PEI, antibody derivatized PEI, and polyethylene glycol PEI (PEG-PEI) derivatives thereof (see for example Ogris et al., 2001, AAPA PharmSci, 3, 1-11; Furgeson et al., 2003, Bioconjugate Chem., 14, 840-847; Kunath et al., 2002, Phramaceutical Research, 19, 810-817; Choi et al., 2001, Bull. Korean Chem. Soc., 22, 46-52; Bettinger et al., 1999, Bioconjugate Chem., 10, 558-561; Peterson et al., 2002, Bioconjugate Chem., 13, 845-854; Erbacher et al., 1999, Journal of Gene Medicine Preprint, 1, 1-18; Godbey et al., 1999, PNAS USA, 96, 5177-5181; Godbey et al., 1999, Journal of Controlled Release, 60, 149-160; Diebold et al., 1999, Journal of Biological Chemistry, 274, 19087-19094; Thomas and Klibanov, 2002, PNAS USA, 99, 14640-14645; and Sagara, U.S. Pat. No. 6,586,524, incorporated by reference herein.

By “pharmaceutically acceptable formulation” or “pharmaceutically acceptable composition” is meant a composition or formulation that allows for the effective distribution of the nucleic acid molecules of the instant invention in the physical location most suitable for their desired activity. Non-limiting examples of agents suitable for formulation with the nucleic acid molecules of the instant invention include: P-glycoprotein inhibitors (such as Pluronic P85); biodegradable polymers, such as poly (DL-lactide-coglycolide) microspheres for sustained release delivery (Emerich, D F et al, 1999, Cell Transplant, 8, 47-58); and loaded nanoparticles, such as those made of polybutylcyanoacrylate. Other non-limiting examples of delivery strategies for the nucleic acid molecules of the instant invention include material described in Boado et al., 1998, J. Pharm. Sci., 87, 1308-1315; Tyler et al., 1999, FEBS Lett., 421, 280-284; Pardridge et al., 1995, PNAS USA., 92, 5592-5596; Boado, 1995, Adv. Drug Delivery Rev., 15, 73-107; Aldrian-Herrada et al., 1998, Nucleic Acids Res., 26, 4910-4916; and Tyler et al., 1999, PNAS USA., 96, 7053-7058.

The invention also features the use of the composition comprising surface-modified liposomes containing poly(ethylene glycol) lipids (PEG-modified, or long-circulating liposomes or stealth liposomes). These formulations offer a method for increasing the accumulation of drugs in target tissues. This class of drug carriers resists opsonization and elimination by the mononuclear phagocytic system (MPS or RES), thereby enabling longer blood circulation times and enhanced tissue exposure for the encapsulated drug (Lasic et al. Chem. Rev. 1995, 95, 2601-2627; Ishiwata et al., Chem. Pharm. Bull. 1995, 43, 1005-1011). Such liposomes have been shown to accumulate selectively in tumors, presumably by extravasation and capture in the neovascularized target tissues (Lasic et al., Science 1995, 267, 1275-1276; Oku et al., 1995, Biochim. Biophys. Acta, 1238, 86-90). The long-circulating liposomes enhance the pharmacokinetics and pharmacodynamics of DNA and RNA, particularly compared to conventional cationic liposomes which are known to accumulate in tissues of the MPS (Liu et al., J. Biol. Chem. 1995, 42, 24864-24870; Choi et al., International PCT Publication No. WO 96/10391; Ansell et al., International PCT Publication No. WO 96/10390; Holland et al., International PCT Publication No. WO 96/10392). Long-circulating liposomes are also likely to protect drugs from nuclease degradation to a greater extent compared to cationic liposomes, based on their ability to avoid accumulation in metabolically aggressive MPS tissues such as the liver and spleen.

The present invention also includes compositions prepared for storage or administration that include a pharmaceutically effective amount of the desired compounds in a pharmaceutically acceptable carrier or diluent. Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro edit. 1985), hereby incorporated by reference herein. For example, preservatives, stabilizers, dyes and flavoring agents can be provided. These include sodium benzoate, sorbic acid and esters of p-hydroxybenzoic acid. In addition, antioxidants and suspending agents can be used.

A pharmaceutically effective dose is that dose required to prevent, inhibit the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) of a disease state. The pharmaceutically effective dose depends on the type of disease, the composition used, the route of administration, the type of mammal being treated, the physical characteristics of the specific mammal under consideration, concurrent medication, and other factors that those skilled in the medical arts will recognize. Generally, an amount between 0.1 mg/kg and 100 mg/kg body weight/day of active ingredients is administered dependent upon potency of the negatively charged polymer.

The nucleic acid molecules of the invention and formulations thereof can be administered orally, topically, parenterally, by inhalation or spray, or rectally in dosage unit formulations containing conventional non-toxic pharmaceutically acceptable carriers, adjuvants and/or vehicles. The term parenteral as used herein includes percutaneous, subcutaneous, intravascular (e.g., intravenous), intramuscular, or intrathecal injection or infusion techniques and the like. In addition, there is provided a pharmaceutical formulation comprising a nucleic acid molecule of the invention and a pharmaceutically acceptable carrier. One or more nucleic acid molecules of the invention can be present in association with one or more non-toxic pharmaceutically acceptable carriers and/or diluents and/or adjuvants, and if desired other active ingredients. The pharmaceutical compositions containing nucleic acid molecules of the invention can be in a form suitable for oral use, for example, as tablets, troches, lozenges, aqueous or oily suspensions, dispersible powders or granules, emulsion, hard or soft capsules, or syrups or elixirs.

Compositions intended for oral use can be prepared according to any method known to the art for the manufacture of pharmaceutical compositions and such compositions can contain one or more such sweetening agents, flavoring agents, coloring agents or preservative agents in order to provide pharmaceutically elegant and palatable preparations. Tablets contain the active ingredient in admixture with non-toxic pharmaceutically acceptable excipients that are suitable for the manufacture of tablets. These excipients can be, for example, inert diluents; such as calcium carbonate, sodium carbonate, lactose, calcium phosphate or sodium phosphate; granulating and disintegrating agents, for example, corn starch, or alginic acid; binding agents, for example starch, gelatin or acacia; and lubricating agents, for example magnesium stearate, stearic acid or talc. The tablets can be uncoated or they can be coated by known techniques. In some cases such coatings can be prepared by known techniques to delay disintegration and absorption in the gastrointestinal tract and thereby provide a sustained action over a longer period. For example, a time delay material such as glyceryl monosterate or glyceryl distearate can be employed.

Formulations for oral use can also be presented as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent, for example, calcium carbonate, calcium phosphate or kaolin, or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium, for example peanut oil, liquid paraffin or olive oil.

Aqueous suspensions contain the active materials in a mixture with excipients suitable for the manufacture of aqueous suspensions. Such excipients are suspending agents, for example sodium carboxymethylcellulose, methylcellulose, hydropropyl-methylcellulose, sodium alginate, polyvinylpyrrolidone, gum tragacanth and gum acacia; dispersing or wetting agents can be a naturally-occurring phosphatide, for example, lecithin, or condensation products of an alkylene oxide with fatty acids, for example polyoxyethylene stearate, or condensation products of ethylene oxide with long chain aliphatic alcohols, for example heptadecaethyleneoxycetanol, or condensation products of ethylene oxide with partial esters derived from fatty acids and a hexitol such as polyoxyethylene sorbitol monooleate, or condensation products of ethylene oxide with partial esters derived from fatty acids and hexitol anhydrides, for example polyethylene sorbitan monooleate. The aqueous suspensions can also contain one or more preservatives, for example ethyl, or n-propyl p-hydroxybenzoate, one or more coloring agents, one or more flavoring agents, and one or more sweetening agents, such as sucrose or saccharin.

Oily suspensions can be formulated by suspending the active ingredients in a vegetable oil, for example arachis oil, olive oil, sesame oil or coconut oil, or in a mineral oil such as liquid paraffin. The oily suspensions can contain a thickening agent, for example beeswax, hard paraffin or cetyl alcohol. Sweetening agents and flavoring agents can be added to provide palatable oral preparations. These compositions can be preserved by the addition of an anti-oxidant such as ascorbic acid

Dispersible powders and granules suitable for preparation of an aqueous suspension by the addition of water provide the active ingredient in admixture with a dispersing or wetting agent, suspending agent and one or more preservatives. Suitable dispersing or wetting agents or suspending agents are exemplified by those already mentioned above. Additional excipients, for example sweetening, flavoring and coloring agents, can also be present.

Pharmaceutical compositions of the invention can also be in the form of oil-in-water emulsions. The oily phase can be a vegetable oil or a mineral oil or mixtures of these. Suitable emulsifying agents can be naturally-occurring gums, for example gum acacia or gum tragacanth, naturally-occurring phosphatides, for example soy bean, lecithin, and esters or partial esters derived from fatty acids and hexitol, anhydrides, for example sorbitan monooleate, and condensation products of the said partial esters with ethylene oxide, for example polyoxyethylene sorbitan monooleate. The emulsions can also contain sweetening and flavoring agents.

Syrups and elixirs can be formulated with sweetening agents, for example glycerol, propylene glycol, sorbitol, glucose or sucrose. Such formulations can also contain a demulcent, a preservative and flavoring and coloring agents. The pharmaceutical compositions can be in the form of a sterile injectable aqueous or oleaginous suspension. This suspension can be formulated according to the known art using those suitable dispersing or wetting agents and suspending agents that have been mentioned above. The sterile injectable preparation can also be a sterile injectable solution or suspension in a non-toxic parentally acceptable diluent or solvent, for example as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that can be employed are water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose, any bland fixed oil can be employed including synthetic mono-or diglycerides. In addition, fatty acids such as oleic acid find use in the preparation of injectables.

The nucleic acid molecules of the invention can also be administered in the form of suppositories, e.g., for rectal administration of the drug. These compositions can be prepared by mixing the drug with a suitable non-irritating excipient that is solid at ordinary temperatures but liquid at the rectal temperature and will therefore melt in the rectum to release the drug. Such materials include cocoa butter and polyethylene glycols.

Nucleic acid molecules of the invention can be administered parenterally in a sterile medium. The drug, depending on the vehicle and concentration used, can either be suspended or dissolved in the vehicle. Advantageously, adjuvants such as local anesthetics, preservatives and buffering agents can be dissolved in the vehicle.

Dosage levels of the order of from about 0.1 mg to about 140 mg per kilogram of body weight per day are useful in the treatment of the above-indicated conditions (about 0.5 mg to about 7 g per subject per day). The amount of active ingredient that can be combined with the carrier materials to produce a single dosage form varies depending upon the host treated and the particular mode of administration. Dosage unit forms generally contain between from about 1 mg to about 500 mg of an active ingredient.

It is understood that the specific dose level for any particular subject depends upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, sex, diet, time of administration, route of administration, and rate of excretion, drug combination and the severity of the particular disease undergoing therapy.

For administration to non-human animals, the composition can also be added to the animal feed or drinking water. It can be convenient to formulate the animal feed and drinking water compositions so that the animal takes in a therapeutically appropriate quantity of the composition along with its diet. It can also be convenient to present the composition as a premix for addition to the feed or drinking water.

The nucleic acid molecules of the present invention can also be administered to a subject in combination with other therapeutic compounds to increase the overall therapeutic effect. The use of multiple compounds to treat an indication can increase the beneficial effects while reducing the presence of side effects.

Alternatively, certain siNA molecules of the instant invention can be expressed within cells from eukaryotic promoters (e.g., Izant and Weintraub, 1985, Science, 229, 345; McGarry and Lindquist, 1986, Proc. Natl. Acad. Sci., USA 83, 399; Scanlon et al., 1991, Proc. Natl. Acad. Sci. USA, 88, 10591-5; Kashani-Sabet et al., 1992, Antisense Res. Dev., 2, 3-15; Dropulic et al., 1992, J. Virol., 66, 1432-41; Weerasinghe et al., 1991, J. Virol., 65, 55314; Ojwang et al., 1992, Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al., 1992, Nucleic Acids Res., 20, 4581-9; Sarver et al., 1990 Science, 247, 1222-1225; Thompson et al., 1995, Nucleic Acids Res., 23, 2259; Good et al., 1997, Gene Therapy, 4, 45. Those skilled in the art realize that any nucleic acid can be expressed in eukaryotic cells from the appropriate DNA/RNA vector. The activity of such nucleic acids can be augmented by their release from the primary transcript by a enzymatic nucleic acid (Draper et al., PCT WO 93/23569, and Sullivan et al., PCT WO 94/02595; Ohkawa et al., 1992, Nucleic Acids Symp. Ser., 27, 15-6; Taira et al., 1991, Nucleic Acids Res., 19, 5125-30; Ventura et al., 1993, Nucleic Acids Res., 21, 3249-55; Chowrira et al., 1994, J. Biol. Chem., 269, 25856.

In another aspect of the invention, RNA molecules of the present invention can be expressed from transcription units (see for example Couture et al., 1996, TIG., 12, 510) inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. siNA expressing viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. In another embodiment, pol III based constructs are used to express nucleic acid molecules of the invention (see for example Thompson, U.S. Pats. Nos. 5,902,880 and 6,146,886). The recombinant vectors capable of expressing the siNA molecules can be delivered as described above, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of nucleic acid molecules. Such vectors can be repeatedly administered as necessary. Once expressed, the siNA molecule interacts with the target mRNA and generates an RNAi response. Delivery of siNA molecule expressing vectors can be systemic, such as by intravenous or intra-muscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell (for a review see Couture et al, 1996, TIG., 12, 510).

In one aspect the invention features an expression vector comprising a nucleic acid sequence encoding at least one siNA molecule of the instant invention. The expression vector can encode one or both strands of a siNA duplex, or a single self-complementary strand that self hybridizes into a siNA duplex. The nucleic acid sequences encoding the siNA molecules of the instant invention can be operably linked in a manner that allows expression of the siNA molecule (see for example Paul et al., 2002, Nature Biotechnology, 19, 505; Miyagishi and Taira, 2002, Nature Biotechnology, 19, 497; Lee et al., 2002, Nature Biotechnology, 19, 500; and Novina et al., 2002, Nature Medicine, advance online publication doi: 10.1038/nm725).

In another aspect, the invention features an expression vector comprising: a) a transcription initiation region (e.g., eukaryotic pol I, II or III initiation region); b) a transcription termination region (e.g., eukaryotic pol I, II or III termination region); and c) a nucleic acid sequence encoding at least one of the siNA molecules of the instant invention, wherein said sequence is operably linked to said initiation region and said termination region in a manner that allows expression and/or delivery of the siNA molecule. The vector can optionally include an open reading frame (ORF) for a protein operably linked on the 5′ side or the 3′-side of the sequence encoding the siNA of the invention; and/or an intron (intervening sequences).

Transcription of the siNA molecule sequences can be driven from a promoter for eukaryotic RNA polymerase I (pol I), RNA polymerase II (pol II), or RNA polymerase III (pol III). Transcripts from pol II or pol III promoters are expressed at high levels in all cells; the levels of a given pol II promoter in a given cell type depends on the nature of the gene regulatory sequences (enhancers, silencers, etc.) present nearby. Prokaryotic RNA polymerase promoters are also used, providing that the prokaryotic RNA polymerase enzyme is expressed in the appropriate cells (Elroy-Stein and Moss, 1990, Proc. Natl. Acad. Sci. USA, 87, 6743-7; Gao and Huang 1993, Nucleic Acids Res., 21, 2867-72; Lieber et al., 1993, Methods Enzymol., 217, 47-66; Zhou et al., 1990, Mol. Cell. Biol., 10, 4529-37). Several investigators have demonstrated that nucleic acid molecules expressed from such promoters can function in mammalian cells (e.g. Kashani-Sabet et al., 1992, Antisense Res. Dev., 2, 3-15; Ojwang et al., 1992, Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al., 1992, Nucleic Acids Res., 20, 4581-9; Yu et al., 1993, Proc. Natl. Acad. Sci. USA, 90, 63404; L'Huillier et al., 1992, EMBO J., 11, 4411-8; Lisziewicz et al., 1993, Proc. Natl. Acad. Sci. U.S. A, 90, 8000-4; Thompson et al., 1995, Nucleic Acids Res., 23, 2259; Sullenger & Cech, 1993, Science, 262, 1566). More specifically, transcription units such as the ones derived from genes encoding U6 small nuclear (snRNA), transfer RNA (tRNA) and adenovirus VA RNA are useful in generating high concentrations of desired RNA molecules such as siNA in cells (Thompson et al., supra; Couture and Stinchcomb, 1996, supra; Noonberg et al., 1994, Nucleic Acid Res., 22, 2830; Noonberg et al., U.S. Pat. No. 5,624,803; Good et al., 1997, Gene Ther., 4, 45; Beigelman et al., International PCT Publication No. WO 96/18736. The above siNA transcription units can be incorporated into a variety of vectors for introduction into mammalian cells, including but not restricted to, plasmid DNA vectors, viral DNA vectors (such as adenovirus or adeno-associated virus vectors), or viral RNA vectors (such as retroviral or alphavirus vectors) (for a review see Couture and Stinchcomb, 1996, supra).

In another aspect the invention features an expression vector comprising a nucleic acid sequence encoding at least one of the siNA molecules of the invention in a manner that allows expression of that siNA molecule. The expression vector comprises in one embodiment; a) a transcription initiation region; b) a transcription termination region; and c) a nucleic acid sequence encoding at least one strand of the siNA molecule, wherein the sequence is operably linked to the initiation region and the termination region in a manner that allows expression and/or delivery of the siNA molecule.

In another embodiment the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an open reading frame; and d) a nucleic acid sequence encoding at least one strand of a siNA molecule, wherein the sequence is operably linked to the 3′-end of the open reading frame and wherein the sequence is operably linked to the initiation region, the open reading frame and the termination region in a manner that allows expression and/or delivery of the siNA molecule. In yet another embodiment, the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; and d) a nucleic acid sequence encoding at least one siNA molecule, wherein the sequence is operably linked to the initiation region, the intron and the termination region in a manner which allows expression and/or delivery of the nucleic acid molecule.

In another embodiment, the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; d) an open reading frame; and e) a nucleic acid sequence encoding at least one strand of a siNA molecule, wherein the sequence is operably linked to the 3′-end of the open reading frame and wherein the sequence is operably linked to the initiation region, the intron, the open reading frame and the termination region in a manner which allows expression and/or delivery of the siNA molecule.

BACE, APP, PIN-1, and PS Biology and Biochemistry

Alzheimer's disease is characterized by the progressive formation of insoluble plaques and vascular deposits in the brain consisting of the 4 kD amyloid β peptide (Aβ). These plaques are characterized by dystrophic neurites that show profound synaptic loss, neurofibrillary tangle formation, and gliosis. Aβ arises from the proteolytic cleavage of the large type I transmembrane protein, β-amyloid precursor protein (APP) (Kang et al., 1987, Nature, 325, 733). Processing of APP to generate Aβ requires two sites of cleavage by a β-secretase and a γ-secretase. β-secretase cleavage of APP results in the cytoplasmic release of a 100 kD soluble amino-terminal fragment, APPsβ, leaving behind a 12 kD transmembrane carboxy-terminal fragment, C99. Alternately, APP can be cleaved by a α-secretase to generate cytoplasmic APPsα and transmembrane C83 fragments. Both remaining transmembrane fragments, C99 and C83, can be further cleaved by a γ-secretase, leading to the release and secretion of Alzheimer's related Aβ and a non-pathogenic peptide, p3, respectively (Vassar et al., 1999, Science, 286, 735-741). Early onset familial Alzheimer's disease is characterized by mutant APP protein with a Met to Leu substitution at position P1, characterized as the “Swedish” familial mutation (Mullan et al., 1992, Nature Genet., 1, 345). This APP mutation is characterized by a dramatic enhancement in β-secretase cleavage (Citron et al., 1992, Nature, 360, 672).

The identification of β-secretase and γ-secretase constituents involved in the release of β-amyloid protein is of primary importance in the development of treatment strategies for Alzheimer's disease. Characterization of α-secretase is also important in this regard since α-secretase cleavage may compete with β-secretase cleavage resulting in changes in the relative amounts of non-pathogenic and pathogenic protein production. Involvement of the two metalloproteases, ADAM 10 and TACE, has been demonstrated in α-cleavage of AAP (Buxbaum et al., 1999, J. Biol. Chem., 273, 27765, and Lammich et al., 1999, Proc. Natl. Acad. Sci. U.S.A., 96, 3922). Studies of γ-secretase activity have demonstrated presenilin dependence (De Stooper et al., 1998, Nature, 391, 387, and De Stooper et al., 1999, Nature, 398, 518), and as such, presenilins have been proposed as γ-secretase even though presenilin does not present proteolytic activity (Wolfe et al., 1999, Nature, 398, 513).

Studies have shown β-secretase cleavage of AAP by the transmembrane aspartic protease beta site APP cleaving enzyme, BACE (Vassar et al., supra). While other potential candidates for β-secretase have been proposed (for review see Evin et al., 1999, Proc. Natl. Acad. Sci. U.S.A., 96, 3922), none have demonstrated the full range of characteristics expected from this enzyme. Studies have shown that BACE expression and localization are as expected for β-secretase, that BACE overexpression in cells results in increased β-secretase cleavage of APP and Swedish APP, that isolated BACE demonstrates site specific proteolytic activity on APP derived peptide substrates, and that antisense mediated endogenous BACE inhibition results in dramatically reduced β-secretaseactivity (Vassar et al., supra).

Current treatment strategies for Alzheimer's disease rely on either the prevention or the alleviation of symptoms and/or the slowing down of disease progression. Two drugs approved in the treatment of Alzheimer's, donepezil (Aricept®) and tacrine (Cognex®), both cholinomimetics, attempt to slow the loss of cognitive ability by increasing the amount of acetylcholine available to the brain. Antioxidant therapy through the use of antioxidant compounds such as alpha-tocopherol (vitamin E), melatonin, and selegeline (Eldepryl®) attempt to slow disease progression by minimizing free radical damage. Estrogen replacement therapy is thought to incur a possible preventative benefit in the development of Alzheimer's disease based on limited data. The use of anti-inflammatory drugs may be associated with a reduced risk of Alzheimer's as well. Calcium channel blockers such as Nimodipine® are considered to have a potential benefit in treating Alzheimer's disease due to protection of nerve cells from calcium overload, thereby prolonging nerve cell survival. Nootropic compounds, such as acetyl-L-camitine (Alcar®) and insulin, have been proposed to have some benefit in treating Alzheimer's due to enhancement of cognitive and memory function based on cellular metabolism.

Whereby the above treatment strategies can all improve quality of life in Alzheimer's patients, there exists an unmet need in the comprehensive treatment and prevention of this disease. As such, there exists the need for therapeutics effective in reversing the physiological changes associated with Alzheimer's disease, specifically, therapeutics that can eliminate and/or reverse the deposition of amyloid β peptide. The use of compounds, such as small nucleic acid molecules (e.g., short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (mRNA), and short hairpin RNA (shRNA) molecules capable of mediating RNA interference (RNAi)), to modulate the expression of proteases that are instrumental in the release of amyloid β peptide, namely β-secretase (BACE), γ-secretase (presenilin), and the amyloid precursor protein (APP), is of therapeutic significance.

EXAMPLES

The following are non-limiting examples showing the selection, isolation, synthesis and activity of nucleic acids of the instant invention.

Example 1 Tandem Synthesis of siNA Constructs

Exemplary siNA molecules of the invention are synthesized in tandem using a cleavable linker, for example, a succinyl-based linker. Tandem synthesis as described herein is followed by a one-step purification process that provides RNAi molecules in high yield. This approach is highly amenable to siNA synthesis in support of high throughput RNAi screening, and can be readily adapted to multi-column or multi-well synthesis platforms.

After completing a tandem synthesis of a siNA oligo and its complement in which the 5′-terminal dimethoxytrityl (5′-O-DMT) group remains intact (trityl on synthesis), the oligonucleotides are deprotected as described above. Following deprotection, the siNA sequence strands are allowed to spontaneously hybridize. This hybridization yields a duplex in which one strand has retained the 5′-O-DMT group while the complementary strand comprises a terminal 5′-hydroxyl. The newly formed duplex behaves as a single molecule during routine solid-phase extraction purification (Trityl-On purification) even though only one molecule has a dimethoxytrityl group. Because the strands form a stable duplex, this dimethoxytrityl group (or an equivalent group, such as other trityl groups or other hydrophobic moieties) is all that is required to purify the pair of oligos, for example, by using a C18 cartridge.

Standard phosphoramidite synthesis chemistry is used up to the point of introducing a tandem linker, such as an inverted deoxy abasic succinate or glyceryl succinate linker (see FIG. 1) or an equivalent cleavable linker. A non-limiting example of linker coupling conditions that can be used includes a hindered base such as diisopropylethylamine (DIPA) and/or DMAP in the presence of an activator reagent such as Bromotripyrrolidinophosphoniumhexaflurorophosphate (PyBrOP). After the linker is coupled, standard synthesis chemistry is utilized to complete synthesis of the second sequence leaving the terminal the 5′-O-DMT intact. Following synthesis, the resulting oligonucleotide is deprotected according to the procedures described herein and quenched with a suitable buffer, for example with 50 mM NaOAc or 1.5M NH₄H₂CO₃.

Purification of the siNA duplex can be readily accomplished using solid phase extraction, for example, using a Waters C18 SepPak 1 g cartridge conditioned with 1 column volume (CV) of acetonitrile, 2 CV H₂O, and 2 CV 50 mM NaOAc. The sample is loaded and then washed with 1 CV H120 or 50 mM NaOAc. Failure sequences are eluted with 1 CV 14% ACN (Aqueous with 50 mM NaOAc and 50 mM NaCl). The column is then washed, for example with 1 CV H₂O followed by on-column detritylation, for example by passing 1 CV of 1% aqueous trifluoroacetic acid (TFA) over the column, then adding a second CV of 1% aqueous TFA to the column and allowing to stand for approximately 10 minutes. The remaining TFA solution is removed and the column washed with H₂O followed by 1 CV 1M NaCl and additional H₂O. The siNA duplex product is then eluted, for example, using 1 CV 20% aqueous CAN.

FIG. 2 provides an example of MALDI-TOF mass spectrometry analysis of a purified siNA construct in which each peak corresponds to the calculated mass of an individual siNA strand of the siNA duplex. The same purified siNA provides three peaks when analyzed by capillary gel electrophoresis (CGE), one peak presumably corresponding to the duplex siNA, and two peaks presumably corresponding to the separate siNA sequence strands. Ion exchange HPLC analysis of the same siNA contract only shows a single peak. Testing of the purified siNA construct using a luciferase reporter assay described below demonstrated the same RNAi activity compared to siNA constructs generated from separately synthesized oligonucleotide sequence strands.

Example 2 Identification of Potential siNA Target Sites in any RNA Sequence

The sequence of an RNA target of interest, such as a viral or human mRNA transcript, is screened for target sites, for example by using a computer folding algorithm. In a non-limiting example, the sequence of a gene or RNA gene transcript derived from a database, such as Genbank, is used to generate siNA targets having complementarity to the target. Such sequences can be obtained from a database, or can be determined experimentally as known in the art. Target sites that are known, for example, those target sites determined to be effective target sites based on studies with other nucleic acid molecules, for example ribozymes or antisense, or those targets known to be associated with a disease or condition such as those sites containing mutations or deletions, can be used to design siNA molecules targeting those sites. Various parameters can be used to determine which sites are the most suitable target sites within the target RNA sequence. These parameters include but are not limited to secondary or tertiary RNA structure, the nucleotide base composition of the target sequence, the degree of homology between various regions of the target sequence, or the relative position of the target sequence within the RNA transcript. Based on these determinations, any number of target sites within the RNA transcript can be chosen to screen siNA molecules for efficacy, for example by using in vitro RNA cleavage assays, cell culture, or animal models. In a non-limiting example, anywhere from 1 to 1000 target sites are chosen within the transcript based on the size of the siNA construct to be used. High throughput screening assays can be developed for screening siNA molecules using methods known in the art, such as with multi-well or multi-plate assays to determine efficient reduction in target gene expression.

Example 3 Selection of siNA Molecule Target Sites in a RNA

The following non-limiting steps can be used to carry out the selection of siNAs targeting a given gene sequence or transcript.

-   1. The target sequence is parsed in silico into a list of all     fragments or subsequences of a particular length, for example 23     nucleotide fragments, contained within the target sequence. This     step is typically carried out using a custom Perl script, but     commercial sequence analysis programs such as Oligo, MacVector, or     the GCG Wisconsin Package can be employed as well. -   2. In some instances the siNAs correspond to more than one target     sequence; such would be the case for example in targeting different     transcripts of the same gene, targeting different transcripts of     more than one gene, or for targeting both the human gene and an     animal homolog. In this case, a subsequence list of a particular     length is generated for each of the targets, and then the lists are     compared to find matching sequences in each list. The subsequences     are then ranked according to the number of target sequences that     contain the given subsequence; the goal is to find subsequences that     are present in most or all of the target sequences. Alternately, the     ranking can identify subsequences that are unique to a target     sequence, such as a mutant target sequence. Such an approach would     enable the use of siNA to target specifically the mutant sequence     and not effect the expression of the normal sequence. -   3. In some instances the siNA subsequences are absent in one or more     sequences while present in the desired target sequence; such would     be the case if the siNA targets a gene with a paralogous family     member that is to remain untargeted. As in case 2 above, a     subsequence list of a particular length is generated for each of the     targets, and then the lists are compared to find sequences that are     present in the target gene but are absent in the untargeted paralog. -   4. The ranked siNA subsequences can be further analyzed and ranked     according to GC content. A preference can be given to sites     containing 30-70% GC, with a further preference to sites containing     40-60% GC. -   5. The ranked siNA subsequences can be further analyzed and ranked     according to self-folding and internal hairpins. Weaker internal     folds are preferred; strong hairpin structures are to be avoided. -   6. The ranked siNA subsequences can be further analyzed and ranked     according to whether they have runs of GGG or CCC in the sequence.     GGG (or even more Gs) in either strand can make oligonucleotide     synthesis problematic and can potentially interfere with RNAi     activity, so it is avoided whenever better sequences are available.     CCC is searched in the target strand because that will place GGG in     the antisense strand. -   7. The ranked siNA subsequences can be further analyzed and ranked     according to whether they have the dinucleotide UU (uridine     dinucleotide) on the 3′-end of the sequence, and/or AA on the 5′-end     of the sequence (to yield 3′ UU on the antisense sequence). These     sequences allow one to design siNA molecules with terminal TT     thymidine dinucleotides. -   8. Four or five target sites are chosen from the ranked list of     subsequences as described above. For example, in subsequences having     23 nucleotides, the right 21 nucleotides of each chosen 23-mer     subsequence are then designed and synthesized for the upper (sense)     strand of the siNA duplex, while the reverse complement of the left     21 nucleotides of each chosen 23-mer subsequence are then designed     and synthesized for the lower (antisense) strand of the siNA duplex     (see Tables H and III). If terminal TT residues are desired for the     sequence (as described in paragraph 7), then the two 3′ terminal     nucleotides of both the sense and antisense strands are replaced by     TT prior to synthesizing the oligos. -   9. The siNA molecules are screened in an in vitro, cell culture or     animal model system to identify the most active siNA molecule or the     most preferred target site within the target RNA sequence. -   10. Other design considerations can be used when selecting target     nucleic acid sequences, see, for example, Reynolds et al., 2004,     Nature Biotechnology Advanced Online Publication, 1 Feb. 2004,     doi:10.1038/nbt936 and Ui-Tei et al., 2004, Nucleic Acids Research,     32, doi:10.1093/nar/gkh247.

In an alternate approach, a pool of siNA constructs specific to a BACE target sequence is used to screen for target sites in cells expressing BACE RNA, such as cultured A549 cells, 7PA2 cells, Chinese hamster ovary (CHO) cells, or APPsw (Swedish type amyloid precursor protein expressing) cells. The general strategy used in this approach is shown in FIG. 9. A non-limiting example of such is a pool comprising sequences having any of SEQ ID NOS 1-1900. Cells expressing BACE (e.g., A549 cells) are transfected with the pool of siNA constructs and cells that demonstrate a phenotype associated with BACE inhibition are sorted. The pool of siNA constructs can be expressed from transcription cassettes inserted into appropriate vectors (see for example FIG. 7 and FIG. 8). The siNA from cells demonstrating a positive phenotypic change (e.g., decreased proliferation, decreased BACE mRNA levels or decreased BACE protein expression), are sequenced to determine the most suitable target site(s) within the target BACE RNA sequence.

Example 4 BACE Targeted siNA Design

siNA target sites were chosen by analyzing sequences of the BACE RNA target and optionally prioritizing the target sites on the basis of folding (structure of any given sequence analyzed to determine siNA accessibility to the target), by using a library of siNA molecules as described in Example 3, or alternately by using an in vitro siNA system as described in Example 6 herein. siNA molecules were designed that could bind each target and are optionally individually analyzed by computer folding to assess whether the siNA molecule can interact with the target sequence. Varying the length of the siNA molecules can be chosen to optimize activity. Generally, a sufficient number of complementary nucleotide bases are chosen to bind to, or otherwise interact with, the target RNA, but the degree of complementarity can be modulated to accommodate siNA duplexes or varying length or base composition. By using such methodologies, siNA molecules can be designed to target sites within any known RNA sequence, for example those RNA sequences corresponding to the any gene transcript.

Chemically modified sNA constructs are designed to provide nuclease stability for systemic administration in vivo and/or improved pharmacokinetic, localization, and delivery properties while preserving the ability to mediate RNAi activity. Chemical modifications as described herein are introduced synthetically using synthetic methods described herein and those generally known in the art. The synthetic siNA constructs are then assayed for nuclease stability in serum and/or cellular/tissue extracts (e.g. liver extracts). The synthetic siNA constructs are also tested in parallel for RNAi activity using an appropriate assay, such as a luciferase reporter assay as described herein or another suitable assay that can quantity RNAi activity. Synthetic siNA constructs that possess both nuclease stability and RNAi activity can be further modified and re-evaluated in stability and activity assays. The chemical modifications of the stabilized active siNA constructs can then be applied to any siNA sequence targeting any chosen RNA and used, for example, in target screening assays to pick lead siNA compounds for therapeutic development (see for example FIG. 11).

Example 5 Chemical Synthesis and Purification of siNA

siNA molecules can be designed to interact with various sites in the RNA message, for example, target sequences within the RNA sequences described herein. The sequence of one strand of the siNA molecule(s) is complementary to the target site sequences described above. The siNA molecules can be chemically synthesized using methods described herein. Inactive siNA molecules that are used as control sequences can be synthesized by scrambling the sequence of the siNA molecules such that it is not complementary to the target sequence. Generally, siNA constructs can by synthesized using solid phase oligonucleotide synthesis methods as described herein (see for example Usman et al., U.S. Pat. Nos. 5,804,683; 5,831,071; 5,998,203; 6,117,657; 6,353,098; 6,362,323; 6,437,117; 6,469,158; Scaringe et al., U.S. Pat. Nos. 6,111,086; 6,008,400; 6,111,086 all incorporated by reference herein in their entirety).

In a non-limiting example, RNA oligonucleotides are synthesized in a stepwise fashion using the phosphoramidite chemistry as is known in the art. Standard phosphoramidite chemistry involves the use of nucleosides comprising any of 5′-O-dimethoxytrityl, 2′-O-tert-butyldimethylsilyl, 3′-O-2-Cyanoethyl N,N-diisopropylphos-phoroamidite groups, and exocyclic amine protecting groups (e.g. N6-benzoyl adenosine, N4 acetyl cytidine, and N2-isobutyryl guanosine). Alternately, 2′-O-Silyl Ethers can be used in conjunction with acid-labile 2′-O-orthoester protecting groups in the synthesis of RNA as described by Scaringe supra. Differing 2′ chemistries can require different protecting groups, for example 2′-deoxy-2′-amino nucleosides can utilize N-phthaloyl protection as described by Usman et al., U.S. Pat. No. 5,631,360, incorporated by reference herein in its entirety).

During solid phase synthesis, each nucleotide is added sequentially (3′- to 5′-direction) to the solid support-bound oligonucleotide. The first nucleoside at the 3′-end of the chain is covalently attached to a solid support (e.g., controlled pore glass or polystyrene) using various linkers. The nucleotide precursor, a ribonucleoside phosphoramidite, and activator are combined resulting in the coupling of the second nucleoside phosphoramidite onto the 5′-end of the first nucleoside. The support is then washed and any unreacted 5′-hydroxyl groups are capped with a capping reagent such as acetic anhydride to yield inactive 5′-acetyl moieties. The trivalent phosphorus linkage is then oxidized to a more stable phosphate linkage. At the end of the nucleotide addition cycle, the 5′-O-protecting group is cleaved under suitable conditions (e.g., acidic conditions for trityl-based groups and Fluoride for silyl-based groups). The cycle is repeated for each subsequent nucleotide.

Modification of synthesis conditions can be used to optimize coupling efficiency, for example by using differing coupling times, differing reagent/phosphoramidite concentrations, differing contact times, differing solid supports and solid support linker chemistries depending on the particular chemical composition of the siNA to be synthesized. Deprotection and purification of the siNA can be performed as is generally described in Deprotection and purification of the siNA can be performed as is generally described in Usman et al., U.S. Pat. No. 5,831,071, U.S. Pat. No. 6,353,098, U.S. Pat. No. 6,437,117, and Bellon et al., U.S. Pat. No. 6,054,576, U.S. Pat. No. 6,162,909, U.S. Pat. No. 6,303,773, or Scaringe supra, incorporated by reference herein in their entireties. Additionally, deprotection conditions can be modified to provide the best possible yield and purity of siNA constructs. For example, applicant has observed that oligonucleotides comprising 2′-deoxy-2′-fluoro nucleotides can degrade under inappropriate deprotection conditions. Such oligonucleotides are deprotected using aqueous methylamine at about 35° C. for 30 minutes. If the 2′-deoxy-2′-fluoro containing oligonucleotide also comprises ribonucleotides, after deprotection with aqueous methylamine at about 35° C. for 30 minutes, TEA-HF is added and the reaction maintained at about 65° C. for an additional 15 minutes.

Example 6 RNAi In Vitro Assay to Assess siNA Activity

An in vitro assay that recapitulates RNAi in a cell-free system is used to evaluate siNA constructs targeting BACE RNA targets. The assay comprises the system described by Tuschl et al., 1999, Genes and Development, 13, 3191-3197 and Zamore et al., 2000, Cell, 101, 25-33 adapted for use with BACE target RNA. A Drosophila extract derived from syncytial blastoderm is used to reconstitute RNAi activity in vitro. Target RNA is generated via in vitro transcription from an appropriate BACE expressing plasmid using T7 RNA polymerase or via chemical synthesis as described herein. Sense and antisense siNA strands (for example 20 uM each) are annealed by incubation in buffer (such as 100 mM potassium acetate, 30 mM HEPES-KOH, pH 7.4, 2 mM magnesium acetate) for 1 minute at 90° C. followed by 1 hour at 37° C., then diluted in lysis buffer (for example 100 mM potassium acetate, 30 mM HEPES-KOH at pH 7.4, 2 mM magnesium acetate). Annealing can be monitored by gel electrophoresis on an agarose gel in TBE buffer and stained with ethidium bromide. The Drosophila lysate is prepared using zero to two-hour-old embryos from Oregon R flies collected on yeasted molasses agar that are dechorionated and lysed. The lysate is centrifuged and the supernatant isolated. The assay comprises a reaction mixture containing 50% lysate [vol/vol], RNA (10-50 pM final concentration), and 10% [vol/vol] lysis buffer containing siNA (10 nM final concentration). The reaction mixture also contains 10 mM creatine phosphate, 10 ug/ml creatine phosphokinase, 100 um GTP, 100 uM UTP, 100 uM CTP, 500 uM ATP, 5 mM DTT, 0.1 U/uL RNasin (Promega), and 100 uM of each amino acid. The final concentration of potassium acetate is adjusted to 100 mM. The reactions are pre-assembled on ice and preincubated at 25° C. for 10 minutes before adding RNA, then incubated at 25° C. for an additional 60 minutes. Reactions are quenched with 4 volumes of 1.25×Passive Lysis Buffer (Promega). Target RNA cleavage is assayed by RT-PCR analysis or other methods known in the art and are compared to control reactions in which siNA is omitted from the reaction.

Alternately, internally-labeled target RNA for the assay is prepared by in vitro transcription in the presence of [alpha-³²P] CTP, passed over a G50 Sephadex column by spin chromatography and used as target RNA without further purification. Optionally, target RNA is 5′-³²P-end labeled using T4 polynucleotide kinase enzyme. Assays are performed as described above and target RNA and the specific RNA cleavage products generated by RNAi are visualized on an autoradiograph of a gel. The percentage of cleavage is determined by PHOSPHOR IMAGER® (autoradiography) quantitation of bands representing intact control RNA or RNA from control reactions without siNA and the cleavage products generated by the assay.

In one embodiment, this assay is used to determine target sites in the BACE RNA target for siNA mediated RNAi cleavage, wherein a plurality of siNA constructs are screened for RNAi mediated cleavage of the BACE RNA target, for example, by analyzing the assay reaction by electrophoresis of labeled target RNA, or by northern blotting, as well as by other methodology well known in the art.

Example 7 Nucleic Acid Inhibition of BACE Target RNA

siNA molecules targeted to the human BACE RNA are designed and synthesized as described above. These nucleic acid molecules can be tested for cleavage activity in vivo, for example, using the following procedure. The target sequences and the nucleotide location within the BACE RNA are given in Tables II and III.

Two formats are used to test the efficacy of siNAs targeting BACE. First, the reagents are tested in cell culture using, for example, cultured A549 cells, 7PA2 cells, Chinese hamster ovary (CHO) cells, APPsw (Swedish type amyloid precursor protein expressing) cells, or SK—N—SH cells, to determine the extent of RNA and protein inhibition. siNA reagents (e.g.; see Tables II and III are selected against the BACE target as described herein. RNA inhibition is measured after delivery of these reagents by a suitable transfection agent to, for example, A549 cells, 7PA2 cells, CHO cells, APPsw cells, or SK—N—SH cells. Relative amounts of target RNA are measured versus actin using real-time PCR monitoring of amplification (e.g., ABI 7700 TAQMAN®). A comparison is made to a mixture of oligonucleotide sequences made to unrelated targets or to a randomized siNA control with the same overall length and chemistry, but randomly substituted at each position. Primary and secondary lead reagents are chosen for the target and optimization performed. After an optimal transfection agent concentration is chosen, a RNA time-course of inhibition is performed with the lead siNA molecule. In addition, a cell-plating format can be used to determine RNA inhibition.

Delivery of siNA to Cells

Cells (e.g., A549 cells, 7PA2 cells, CHO cells, APPsw cells, or SK—N—SH cells) are seeded, for example, at 1×10⁵ cells per well of a six-well dish in EGM-2 (BioWhittaker) the day before transfection. siNA (final concentration, for example 20 nM) and cationic lipid (e.g., final concentration 2 μg/ml) are complexed in EGM basal media (Bio Whittaker) at 37° C. for 30 minutes in polystyrene tubes. Following vortexing, the complexed siNA is added to each well and incubated for the times indicated. For initial optimization experiments, cells are seeded, for example, at 1×10³ in 96 well plates and siNA complex added as described. Efficiency of delivery of siNA to cells is determined using a fluorescent siNA complexed with lipid. Cells in 6-well dishes are incubated with siNA for 24 hours, rinsed with PBS and fixed in 2% paraformaldehyde for 15 minutes at room temperature. Uptake of siNA is visualized using a fluorescent microscope.

TAQMAN® (Real-Time PCR Monitoring of Amplification) and Lightcycler Quantification of mRNA

Total RNA is prepared from cells following siNA delivery, for example, using Qiagen RNA purification kits for 6-well or Rneasy extraction kits for 96-well assays. For TAQMAN® analysis (real-time PCR monitoring of amplification), dual-labeled probes are synthesized with the reporter dye, FAM or JOE, covalently linked at the 5′-end and the quencher dye TAMRA conjugated to the 3′-end. One-step RT-PCR amplifications are performed on, for example, an ABI PRISM 7700 Sequence Detector using 50 μl reactions consisting of 10 μl total RNA, 100 nM forward primer, 900 nM reverse primer, 100 nM probe, 1×TaqMan PCR reaction buffer (PE-Applied Biosystems), 5.5 mM MgCl₂, 300 μM each dATP, dCTP, dGTP, and dTTP, 10U RNase Inhibitor (Promega), 1.25U AMPLITAQ GOLD® (DNA polymerase) (PE-Applied Biosystems) and 10U M-MLV Reverse Transcriptase (Promega). The thermal cycling conditions can consist of 30 minutes at 48° C., 10 minutes at 95° C., followed by 40 cycles of 15 seconds at 95° C. and 1 minute at 60° C. Quantitation of mRNA levels is determined relative to standards generated from serially diluted total cellular RNA (300, 100, 33, 11 ng/rxn) and normalizing to β-actin or GAPDH mRNA in parallel TAQMAN® reactions (real-time PCR monitoring of amplification). For each gene of interest an upper and lower primer and a fluorescently labeled probe are designed. Real time incorporation of SYBR Green I dye into a specific PCR product can be measured in glass capillary tubes using a lightcyler. A standard curve is generated for each primer pair using control cRNA. Values are represented as relative expression to GAPDH in each sample.

Western Blotting

Nuclear extracts can be prepared using a standard micro preparation technique (see for example Andrews and Faller, 1991, Nucleic Acids Research, 19, 2499). Protein extracts from supernatants are prepared, for example using TCA precipitation. An equal volume of 20% TCA is added to the cell supernatant, incubated on ice for 1 hour and pelleted by centrifugation for 5 minutes. Pellets are washed in acetone, dried and resuspended in water. Cellular protein extracts are run on a 10% Bis-Tris NuPage (nuclear extracts) or 4-12% Tris-Glycine (supernatant extracts) polyacrylamide gel and transferred onto nitro-cellulose membranes. Non-specific binding can be blocked by incubation, for example, with 5% non-fat milk for 1 hour followed by primary antibody for 16 hour at 4° C. Following washes, the secondary antibody is applied, for example (1:10,000 dilution) for 1 hour at room temperature and the signal detected with SuperSignal reagent (Pierce).

Example 8 Models useful to Evaluate the Down-Regulation of BACE Gene Expression

Cell Culture

Vassar et al., 1999, Science, 286, 735-741, describe a cell culture model for studying BACE inhibition. Specific antisense nucleic acid molecules targeting BACE mRNA were used for inhibition studies of endogenous BACE expression in 101 cells and APPsw (Swedish type amyloid precursor protein expressing) cells via lipid mediated transfection. Antisense treatment resulted in dramatic reduction of both BACE mRNA by Northern blot analysis, and APPsβsw (“Swedish” type β-secretase cleavage product) by ELISA, with maximum inhibition of both parameters at 75-80%. This model was also used to study the effect of BACE inhibition on amyloid β-peptide production in APPsw cells. Similarly, such a model can be used to screen siRNA molecules of the instant invention for efficacy and potency.

In several cell culture systems, cationic lipids have been shown to enhance the bioavailability of oligonucleotides to cells in culture (Bennet, et al., 1992, Mol. Pharmacology, 41, 1023-1033). In one embodiment, siNA molecules of the invention are complexed with cationic lipids for cell culture experiments. siNA and cationic lipid mixtures are prepared in serum-free DMEM immediately prior to addition to the cells. DMEM plus additives are warmed to room temperature (about 20-25° C.) and cationic lipid is added to the final desired concentration and the solution is vortexed briefly. siNA molecules are added to the final desired concentration and the solution is again vortexed briefly and incubated for 10 minutes at room temperature. In dose response experiments, the RNA/lipid complex is serially diluted into DMEM following the 10 minute incubation.

Animal Models

Evaluating the efficacy of anti-BACE agents in animal models is an important prerequisite to human clinical trials. Games et al., 1995, Nature, 373, 523-527, describe a transgenic mouse model in which mutant human familial type APP (Phe 717 instead of Val) is overexpressed. This model results in mice that progressively develop many of the pathological hallmarks of Alzheimer's disease, and as such, provides a model for testing therapeutic drugs, including siNA constructs of the instant invention.

Example 9 RNAi Mediated Inhibition of BACE, APP, PS1 or PS2 Expression in Cell Culture

Inhibition of BACE, APP, PSI, or PS2 RNA Expression using siNA Targeting BACE, APP, PS1, or PS2 RNA

siNA constructs (Table III) are tested for efficacy in reducing BACE, APP, PS1 or PS2 RNA expression in A549 or SK—N—SH cells. Cells are plated approximately 24 hours before transfection in 96-well plates at 5,000-7,500 cells/well, 1001 μl/well, such that at the time of transfection cells are 70-90% confluent. For transfection, annealed siNAs are mixed with the transfection reagent (Lipofectamine 2000, Invitrogen) in a volume of 50 μl/well and incubated for 20 minutes at room temperature. The siNA transfection mixtures are added to cells to give a final siNA concentration of 25 nM in a volume of 150 μl. Each siNA transfection mixture is added to 3 wells for triplicate siNA treatments. Cells are incubated at 37° for 24 hours in the continued presence of the siNA transfection mixture. At 24 hours, RNA is prepared from each well of treated cells. The supernatants with the transfection mixtures are first removed and discarded, then the cells are lysed and RNA prepared from each well. Target gene expression following treatment is evaluated by RT-PCR for the target gene and for a control gene (36B4, an RNA polymerase subunit) for normalization. The triplicate data is averaged and the standard deviations determined for each treatment. Normalized data are graphed and the percent reduction of target mRNA by active siNAs in comparison to their respective inverted control siNAs is determined.

In a non-limiting example, using the method described above, siNA constructs were screened for activity (see FIG. 22) and compared to untreated cells, scrambled siNA control constructs (Scram1 and Scram2), and cells transfected with lipid alone (transfection control). As shown in FIG. 22, the siNA constructs show significant reduction of BACE RNA expression. Leads generated from such a screen are then further assayed. In a non-limiting example, siNA constructs comprising ribonucleotides and 3′-terminal dithymidine caps are assayed along with a chemically modified siNA construct comprising 2′-deoxy-2′-fluoro pyrimidine nucleotides and purine ribonucleotides, in which the sense strand of the siNA is further modified with 5′ and 3′-terminal inverted deoxyabasic caps and the antisense strand comprises a 3′-terminal phosphorothioate internucleotide linkage. Additional stabilization chemistries as described in Table IV are similarly assayed for activity. These siNA constructs are compared to appropriate matched chemistry inverted controls. In addition, the siNA constructs are also compared to untreated cells, cells transfected with lipid and scrambled siNA constructs, and cells transfected with lipid alone (transfection control).

Using the method described above, a lead siNA construct (31007/31083) chosen from the screen described in FIG. 22 above was further modified using chemical modifications described in Table IV herein. Results are shown in FIG. 23. A549 cells were transfected with 0.25 ug/well of lipid complexed with 25 nM siNA. Chemically modified constructs having Stab 4/5 chemistry (31378/31381) and Stab 7/11 chemistry (31384/31387) (solid bars; see Table IV) were tested for efficacy compared to matched chemistry inverted controls (open bars; sequences of the siNA constructs shown in Table m). The original lead siNA construct (31007/31083) and the Stab 4/5 and Stab 7/11 constructs were compared to untreated cells, scrambled siNA control constructs (Scram1 and Scram2), and cells transfected with lipid alone (transfection control). As shown in FIG. 23, the original lead construct and the Stab 4/5 and Stab 7/11 modified siNA constructs all show significant reduction of BACE RNA expression.

FIG. 24 shows a non-limiting example of the reduction of APP mRNA in SK—N—SH cells mediated by siNAs that target APP mRNA. SK—N—SH cells were transfected with 0.25 ug/well of lipid complexed with 25 nM siNA. Active chemically modified siNA constructs (solid bars; see Tables m and IV) were compared to untreated cells, matched chemistry irrelevant siNA control constructs (IC-1), and cells transfected with lipid alone (transfection control). As shown in FIG. 24, the siNA constructs significantly reduce APP RNA expression compared with irrelevant siNA control and transfection control constructs.

FIG. 25 shows a non-limiting example of the reduction of PSEN1 mRNA in SK—N—SH cells mediated by siNAs that target PSEN1 mRNA. SK—N—SH cells were transfected with 0.25 ug/well of lipid complexed with 25 nM siNA. Active chemically modified siNA constructs (solid bars; see Tables III and IV) were compared to untreated cells, matched chemistry irrelevant siNA control constructs (IC-1), and cells transfected with lipid alone (transfection control). As shown in FIG. 25, the siNA constructs significantly reduce PSEN1 RNA expression compared with irrelevant siNA control and transfection control constructs.

FIG. 26 shows a non-limiting example of the reduction of PSEN2 mRNA in SK—N—SH cells mediated by siNAs that target PSEN2 mRNA. SK—N—SH cells were transfected with 0.25 ug/well of lipid complexed with 25 nM siNA. Active chemically modified siNA constructs (solid bars; see Tables III and IV) were compared to untreated cells, matched chemistry irrelevant siNA control constructs (IC-1), and cells transfected with lipid alone (transfection control). As shown in FIG. 26, the siNA constructs significantly reduce PSEN2 RNA expression compared with irrelevant sNA control and transfection control constructs.

Example 10 Indications

Particular degenerative and disease states that can be associated with BACE, APP, PIN-1, PS-1 and/or PS-2 expression modulation include but are not limited to: Alzheimer's disease, dementia, stroke (CVA) and any other diseases or conditions that are related to the levels of BACE, APP, PIN-1, PS-1 and/or PS-2 in a cell or tissue, alone or in combination with other therapies. The reduction of BACE, APP, PIN-1, PS-1 and/or PS-2 expression (specifically BACE, APP, PIN-1, PS-1 and/or PS-2 RNA levels) and thus reduction in the level of the respective protein relieves, to some extent, the symptoms of the disease or condition.

Those skilled in the art will recognize that other drug compounds and therapies may be readily combined with or used in conjuction with the nucleic acid molecules of the instant invention (e.g., siNA molecules) are hence within the scope of the instant invention.

Example 11 Diagnostic Uses

The siNA molecules of the invention can be used in a variety of diagnostic applications, such as in the identification of molecular targets (e.g., RNA) in a variety of applications, for example, in clinical, industrial, environmental, agricultural and/or research settings. Such diagnostic use of siNA molecules involves utilizing reconstituted RNAi systems, for example, using cellular lysates or partially purified cellular lysates. siNA molecules of this invention can be used as diagnostic tools to examine genetic drift and mutations within diseased cells or to detect the presence of endogenous or exogenous, for example viral, RNA in a cell. The close relationship between siNA activity and the structure of the target RNA allows the detection of mutations in any region of the molecule, which alters the base-pairing and three-dimensional structure of the target RNA. By using multiple siNA molecules described in this invention, one can map nucleotide changes, which are important to RNA structure and function in vitro, as well as in cells and tissues. Cleavage of target RNAs with siNA molecules can be used to inhibit gene expression and define the role of specified gene products in the progression of disease or infection. In this manner, other genetic targets can be defined as important mediators of the disease. These experiments will lead to better treatment of the disease progression by affording the possibility of combination therapies (e.g., multiple siNA molecules targeted to different genes, siNA molecules coupled with known small molecule inhibitors, or intermittent treatment with combinations siNA molecules and/or other chemical or biological molecules). Other in vitro uses of siNA molecules of this invention are well known in the art, and include detection of the presence of mRNAs associated with a disease, infection, or related condition. Such RNA is detected by determining the presence of a cleavage product after treatment with a siNA using standard methodologies, for example, fluorescence resonance emission transfer (FRET).

In a specific example, siNA molecules that cleave only wild-type or mutant forms of the target RNA are used for the assay. The first siNA molecules (i.e., those that cleave only wild-type forms of target RNA) are used to identify wild-type RNA present in the sample and the second siNA molecules (i.e., those that cleave only mutant forms of target RNA) are used to identify mutant RNA in the sample. As reaction controls, synthetic substrates of both wild-type and mutant RNA are cleaved by both siNA molecules to demonstrate the relative siNA efficiencies in the reactions and the absence of cleavage of the “non-targeted” RNA species. The cleavage products from the synthetic substrates also serve to generate size markers for the analysis of wild-type and mutant RNAs in the sample population. Thus, each analysis requires two siNA molecules, two substrates and one unknown sample, which is combined into six reactions. The presence of cleavage products is determined using an RNase protection assay so that full-length and cleavage fragments of each RNA can be analyzed in one lane of a polyacrylamide gel. It is not absolutely required to quantify the results to gain insight into the expression of mutant RNAs and putative risk of the desired phenotypic changes in target cells. The expression of mRNA whose protein product is implicated in the development of the phenotype (i.e., disease related or infection related) is adequate to establish risk. If probes of comparable specific activity are used for both transcripts, then a qualitative comparison of RNA levels is adequate and decreases the cost of the initial diagnosis. Higher mutant form to wild-type ratios are correlated with higher risk whether RNA levels are compared qualitatively or quantitatively.

All patents and publications mentioned in the specification are indicative of the levels of skill of those skilled in the art to which the invention pertains. All references cited in this disclosure are incorporated by reference to the same extent as if each reference had been incorporated by reference in its entirety individually.

One skilled in the art would readily appreciate that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. The methods and compositions described herein as presently representative of preferred embodiments are exemplary and are not intended as limitations on the scope of the invention. Changes therein and other uses will occur to those skilled in the art, which are encompassed within the spirit of the invention, are defined by the scope of the claims.

It will be readily apparent to one skilled in the art that varying substitutions and modifications can be made to the invention disclosed herein without departing from the scope and spirit of the invention. Thus, such additional embodiments are within the scope of the present invention and the following claims. The present invention teaches one skilled in the art to test various combinations and/or substitutions of chemical modifications described herein toward generating nucleic acid constructs with improved activity for mediating RNAi activity. Such improved activity can comprise improved stability, improved bioavailability, and/or improved activation of cellular responses mediating RNAi. Therefore, the specific embodiments described herein are not limiting and one skilled in the art can readily appreciate that specific combinations of the modifications described herein can be tested without undue experimentation toward identifying siNA molecules with improved RNAi activity.

The invention illustratively described herein suitably can be practiced in the absence of any element or elements, limitation or limitations that are not specifically disclosed herein. Thus, for example, in each instance herein any of the terms “comprising”, “consisting essentially of”, and “consisting of” may be replaced with either of the other two terms. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention that in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments, optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the description and the appended claims.

In addition, where features or aspects of the invention are described in terms of Markush groups or other grouping of alternatives, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group or other group. TABLE I Accession Numbers NM_012104 Homo sapiens beta-site APP-cleaving enzyme (BACE), transcript variant a, mRNA gi|21040369|ref|NM_012104.2|[21040369] NM_006222 Homo sapiens protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1-like (PIN1L), mRNA gi|5453899|ref|NM_006222.1|[5453899] L76517 Homo sapiens (clone cc44) senilin 1 (PS1; S182) mRNA, complete cds gi|1479973|gb|L76517.1|HUMPS1MRNA[1479973] L43964 Homo sapiens (clone F-T03796) STM-2 mRNA, complete cds gi|951202|gb|L43964.1|HUMSTM2R[951202] NM_138973 Homo sapiens beta-site APP-cleaving enzyme (BACE), transcript variant d, mRNA gi|21040367|ref|NM_138973.1|[21040367] NM_138972 Homo sapiens beta-site APP-cleaving enzyme (BACE), transcript variant b, mRNA gi|21040365|ref|NM_138972.1|[21040365] NM_138971 Homo sapiens beta-site APP-cleaving enzyme (BACE), transcript variant c, mRNA gi|21040363|ref|NM_138971.1|[21040363] AK075049 Homo sapiens cDNA FLJ90568 fis, clone OVARC1001570, highly similar to Homo sapiens beta-site APP cleaving enzyme (BACE) mRNA gi|22760888|dbj|AK075049.1|[22760888] AF527782 Homo sapiens beta-site APP-cleaving enzyme (BACE) mRNA, partial cds, alternatively spliced gi|22094870|gb|AF527782.1|[22094870] AF324837 Homo sapiens beta-site APP cleaving enzyme mRNA, partial cds, alternatively spliced gi|21449275|gb|AF324837.1|[21449275] AF338817 Homo sapiens beta-site APP cleaving enzyme type C mRNA, complete cds gi|13699247|gb|AF338817.1|[13699247] AF338816 Homo sapiens beta-site APP cleaving enzyme type B mRNA, complete cds gi|13699245|gb|AF338816.1|[13699245] AB050438 Homo sapiens BACE mRNA for beta-site APP cleaving enzyme I-432, complete cds gi|13568410|dbj|AB050438.1|[13568410] AB050437 Homo sapiens BACE mRNA for beta-site APP cleaving enzyme I-457, complete cds gi|13568408|dbj|AB050437.1|[13568408] AB050436 Homo sapiens BACE mRNA for beta-site APP cleaving enzyme I-476, complete cds gi|13568406|dbj|AB050436.1|[13568406] AF190725 Homo sapiens beta-site APP cleaving enzyme (BACE) mRNA, complete cds gi|6118538|gb|AF190725.1|AF190725[6118538] NM_007319 Homo sapiens presenilin 1 (Alzheimer disease 3) (PSEN1), transcript variant I-374., mRNA gi|7549814|ref|NM_007319.1|[7549814] NM_138992 Homo sapiens beta-site APP-cleaving enzyme 2 (BACE2), transcript variant b, mRNA gi|21040361|ref|NM_138992.1|[21040361] NM_138991 Homo sapiens beta-site APP-cleaving enzyme 2 (BACE2), transcript variant c, mRNA gi|21040359|ref|NM_138991.1|[21040359] NM_012105 Homo sapiens beta-site APP-cleaving enzyme 2 (BACE2), transcript variant a, mRNA gi|21040358|ref|NM_012105.3|[21040358] AB066441 Homo sapiens APP mRNA for amyloid precursor protein, partial cds, D678N mutant gi|16904654|dbj|AB066441.1|[16904654] AB050438 Homo sapiens BACE mRNA for beta-site APP cleaving enzyme I-432, complete cds gi|13568410|dbj|AB050438.1|[13568410] AB050437 Homo sapiens BACE mRNA for beta-site APP cleaving enzyme I-457, complete cds gi|13568408|dbj|AB050437.1|[13568408] AB050436 Homo sapiens BACE mRNA for beta-site APP cleaving enzyme I-476, complete cds gi|13568406|dbj|AB050436.1|[13568406] NM_012486 Homo sapiens presenilin 2 (Alzheimer disease 4) (PSEN2), transcript variant 2, mRNA gi|7108359|ref|NM_012486.1|[7108359] NM_000447 Homo sapiens presenilin 2 (Alzheimer disease 4) (PSEN2), transcript variant 1, mRNA gi|4506164|ref|NM_000447.1|[4506164] AF188277 Homo sapiens aspartyl protease (BACE2) mRNA, complete cds, alternatively spliced gi|7025334|gb|AF188277.1|AF188277[7025334] AF188276 Homo sapiens aspartyl protease (BACE2) mRNA, complete cds, alternatively spliced gi|7025332|gb|AF188276.1|AF188276[7025332] AF178532 Homo sapiens aspartyl protease (BACE2) mRNA, complete cds gi|6851265|gb|AF178532.1|AF178532[6851265] D87675 Homo sapiens DNA for amyloid precursor protein, complete cds gi|2429080|dbj|D87675.1|[2429080] AF201468 Homo sapiens APP beta-secretase mRNA, complete cds gi|6601444|gb|AF201468.1|AF201468[6601444] AF190725 Homo sapiens beta-site APP cleaving enzyme (BACE) mRNA, complete cds gi|6118538|gb|AF190725.1|AF190725[6118538] E14707 DNA encoding a mutated amyloid precursor protein gi|5709390|dbj|E14707.1||pat|JP|1998001499|1[5709390] AF168956 Homo sapiens amyloid precursor protein homolog HSD-2 mRNA, complete cds gi|5702387|gb|AF168956.1|AF168956[5702387] S60099 APPH = amyloid precursor protein homolog [human, placenta, mRNA, 3727 nt] gi|300168|bbm|300685|bbs|131198|gb|S60099.1|S60099[300 168] U50939 Human amyloid precursor protein-binding protein 1 mRNA, complete cds gi|1314559|gb|U50939.1|HSU50939[1314559] NM_000484 Homo sapiens amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease) (APP), transcript variant 1, mRNA gi|41406053|ref|NM_000484.2|[41406053] BC018937 Homo sapiens amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease), mRNA (cDNA clone IMAGE: 4126584) gi|39645179|gb|BC018937.2|[39645179] NM_201413 Homo sapiens amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease) (APP), transcript variant 2, mRNA gi|41406054|ref|NM_201413.1|[41406054] NM_201414 Homo sapiens amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease) (APP), transcript variant 3, mRNA gi|41406056|ref|NM_201414.1|[41406056] BC065529 Homo sapiens amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease), transcript variant 2, mRNA (cDNA clone MGC: 75167 IMAGE: 6152423), complete cds gi|41350938|gb|BC065529.1|[41350938] Y00264 Human mRNA for amyloid A4 precursor of Alzheimer's disease gi|28525|emb|Y00264.1|HSAFPA4[28525] AF282245 Homo sapiens amyloid precursor protein 639 (APP639) mRNA, complete cds gi|33339673|gb|AF282245.1|[33339673] X06989 Homo sapiens mRNA for amyloid A4 protein (APP gene) gi|28720|emb|X06989.1|HSAPA4R[28720]

TABLE II APP, BACE, PSEN1, PSEN2 siNA AND TARGET SEQUENCES APP NM_000484 Seq Seq Seq Pos Seq ID UPos Upper seq ID LPos Lower seq ID 3 UUUCCUCGGCAGCGGUAGG 1 3 UUUCCUCGGCAGCGGUAGG 1 21 CCUACCGCUGCCGAGGAAA 200 21 GCGAGAGCACGCGGAGGAG 2 21 GCGAGAGCACGCGGAGGAG 2 39 CUCCUCCGCGUGCUCUCGC 201 39 GCGUGCGCGGGGGCCCCGG 3 39 GCGUGCGCGGGGGCCCCGG 3 57 CCGGGGCCCCCGCGCACGC 202 57 GGAGACGGCGGCGGUGGCG 4 57 GGAGACGGCGGCGGUGGCG 4 75 CGCCACCGCCGCCGUCUCC 203 75 GGCGCGGGCAGAGCAAGGA 5 75 GGCGCGGGCAGAGCAAGGA 5 93 UCCUUGCUCUGCCCGCGCC 204 93 ACGCGGCGGAUCCCACUCG 6 93 ACGCGGCGGAUCCCACUCG 6 111 CGAGUGGGAUCCGCCGCGU 205 111 GCACAGCAGCGCACUCGGU 7 111 GCACAGCAGCGCACUCGGU 7 129 ACCGAGUGCGCUGCUGUGC 206 129 UGCCCCGCGCAGGGUCGCG 8 129 UGCCCCGCGCAGGGUCGCG 8 147 CGCGACCCUGCGCGGGGCA 207 147 GAUGCUGCCCGGUUUGGCA 9 147 GAUGCUGCCCGGUUUGGCA 9 165 UGCCAAACCGGGCAGCAUC 208 165 ACUGCUCCUGCUGGCCGCC 10 165 ACUGCUCCUGCUGGCCGCC 10 183 GGCGGCCAGCAGGAGCAGU 209 183 CUGGACGGCUCGGGCGCUG 11 183 CUGGACGGCUCGGGCGCUG 11 201 CAGCGCCCGAGCCGUCCAG 210 201 GGAGGUACCCACUGAUGGU 12 201 GGAGGUACCCACUGAUGGU 12 219 ACCAUCAGUGGGUACCUCC 211 219 UAAUGCUGGCCUGCUGGCU 13 219 UAAUGCUGGCCUGCUGGCU 13 237 AGCCAGCAGGCCAGCAUUA 212 237 UGAACCCCAGAUUGCCAUG 14 237 UGAACCCCAGAUUGCCAUG 14 255 CAUGGCAAUCUGGGGUUCA 213 255 GUUCUGUGGCAGACUGAAC 15 255 GUUCUGUGGCAGACUGAAC 15 273 GUUCAGUCUGCCACAGAAC 214 273 CAUGCACAUGAAUGUCCAG 16 273 CAUGCACAUGAAUGUCCAG 16 291 CUGGACAUUCAUGUGCAUG 215 291 GAAUGGGAAGUGGGAUUCA 17 291 GAAUGGGAAGUGGGAUUCA 17 309 UGAAUCCCACUUCCCAUUC 216 309 AGAUCCAUCAGGGACCAAA 18 309 AGAUCCAUCAGGGACCAAA 18 327 UUUGGUCCCUGAUGGAUCU 217 327 AACCUGCAUUGAUACCAAG 19 327 AACCUGCAUUGAUACCAAG 19 345 CUUGGUAUCAAUGCAGGUU 218 345 GGAAGGCAUCCUGCAGUAU 20 345 GGAAGGCAUCCUGCAGUAU 20 363 AUACUGCAGGAUGCCUUCC 219 363 UUGCCAAGAAGUCUACCCU 21 363 UUGCCAAGAAGUCUACCCU 21 381 AGGGUAGACUUCUUGGCAA 220 381 UGAACUGCAGAUCACCAAU 22 381 UGAACUGCAGAUCACCAAU 22 399 AUUGGUGAUCUGCAGUUCA 221 399 UGUGGUAGAAGCCAACCAA 23 399 UGUGGUAGAAGCCAACCAA 23 417 UUGGUUGGCUUCUACCACA 222 417 ACCAGUGACCAUCCAGAAC 24 417 ACCAGUGACCAUCCAGAAC 24 435 GUUCUGGAUGGUCACUGGU 223 435 CUGGUGCAAGCGGGGCCGC 25 435 CUGGUGCAAGCGGGGCCGC 25 453 GCGGCCCCGCUUGCACCAG 224 453 CAAGCAGUGCAAGACCCAU 26 453 CAAGCAGUGCAAGACCCAU 26 471 AUGGGUCUUGCACUGCUUG 225 471 UCCCCACUUUGUGAUUCCC 27 471 UCCCCACUUUGUGAUUCCC 27 489 GGGAAUCACAAAGUGGGGA 226 489 CUACCGCUGCUUAGUUGGU 28 489 CUACCGCUGCUUAGUUGGU 28 507 ACCAACUAAGCAGCGGUAG 227 507 UGAGUUUGUAAGUGAUGCC 29 507 UGAGUUUGUAAGUGAUGCC 29 525 GGCAUCACUUACAAACUCA 228 525 CCUUCUCGUUCCUGACAAG 30 525 CCUUCUCGUUCCUGACAAG 30 543 CUUGUCAGGAACGAGAAGG 229 543 GUGCAAAUUCUUACACCAG 31 543 GUGCAAAUUCUUACACCAG 31 561 CUGGUGUAAGAAUUUGCAC 230 561 GGAGAGGAUGGAUGUUUGC 32 561 GGAGAGGAUGGAUGUUUGC 32 579 GCAAACAUCCAUCCUCUCC 231 579 CGAAACUCAUCUUCACUGG 33 579 CGAAACUCAUCUUCACUGG 33 597 CCAGUGAAGAUGAGUUUCG 232 597 GCACACCGUCGCCAAAGAG 34 597 GCACACCGUCGCCAAAGAG 34 615 CUCUUUGGCGACGGUGUGC 233 615 GACAUGCAGUGAGAAGAGU 35 615 GACAUGCAGUGAGAAGAGU 35 633 ACUCUUCUCACUGCAUGUC 234 633 UACCAACUUGCAUGACUAC 36 633 UACCAACUUGCAUGACUAC 36 651 GUAGUCAUGCAAGUUGGUA 235 651 CGGCAUGUUGCUGCCCUGC 37 651 CGGCAUGUUGCUGCCCUGC 37 669 GCAGGGCAGCAACAUGCCG 236 669 CGGAAUUGACAAGUUCCGA 38 669 CGGAAUUGACAAGUUCCGA 38 687 UCGGAACUUGUCAAUUCCG 237 687 AGGGGUAGAGUUUGUGUGU 39 687 AGGGGUAGAGUUUGUGUGU 39 705 ACACACAAACUCUACCCCU 238 705 UUGCCCACUGGCUGAAGAA 40 705 UUGCCCACUGGCUGAAGAA 40 723 UUCUUCAGCCAGUGGGCAA 239 723 AAGUGACAAUGUGGAUUCU 41 723 AAGUGACAAUGUGGAUUCU 41 741 AGAAUCCACAUUGUCACUU 240 741 UGCUGAUGCGGAGGAGGAU 42 741 UGCUGAUGCGGAGGAGGAU 42 759 AUCCUCCUCCGCAUCAGCA 241 759 UGACUCGGAUGUCUGGUGG 43 759 UGACUCGGAUGUCUGGUGG 43 777 CCACCAGACAUCCGAGUCA 242 777 GGGCGGAGCAGACACAGAC 44 777 GGGCGGAGCAGACACAGAC 44 795 GUCUGUGUCUGCUCCGCCC 243 795 CUAUGCAGAUGGGAGUGAA 45 795 CUAUGCAGAUGGGAGUGAA 45 813 UUCACUCCCAUCUGCAUAG 244 813 AGACAAAGUAGUAGAAGUA 46 813 AGACAAAGUAGUAGAAGUA 46 831 UACUUCUACUACUUUGUCU 245 831 AGCAGAGGAGGAAGAAGUG 47 831 AGCAGAGGAGGAAGAAGUG 47 849 CACUUCUUCCUCCUCUGCU 246 849 GGCUGAGGUGGAAGAAGAA 48 849 GGCUGAGGUGGAAGAAGAA 48 867 UUCUUCUUCCACCUCAGCC 247 867 AGAAGCCGAUGAUGACGAG 49 867 AGAAGCCGAUGAUGACGAG 49 885 CUCGUCAUCAUCGGCUUCU 248 885 GGACGAUGAGGAUGGUGAU 50 885 GGACGAUGAGGAUGGUGAU 50 903 AUCACCAUCCUCAUCGUCC 249 903 UGAGGUAGAGGAAGAGGCU 51 903 UGAGGUAGAGGAAGAGGCU 51 921 AGCCUCUUCCUCUACCUCA 250 921 UGAGGAACCCUACGAAGAA 52 921 UGAGGAACCCUACGAAGAA 52 939 UUCUUCGUAGGGUUCCUCA 251 939 AGCCACAGAGAGAACCACC 53 939 AGCCACAGAGAGAACCACC 53 957 GGUGGUUCUCUCUGUGGCU 252 957 CAGCAUUGCCACCACCACC 54 957 CAGCAUUGCCACCACCACC 54 975 GGUGGUGGUGGCAAUGCUG 253 975 CACCACCACCACAGAGUCU 55 975 CACCACCACCACAGAGUCU 55 993 AGACUCUGUGGUGGUGGUG 254 993 UGUGGAAGAGGUGGUUCGA 56 993 UGUGGAAGAGGUGGUUCGA 56 1011 UCGAACCACCUCUUCCACA 255 1011 AGAGGUGUGCUCUGAACAA 57 1011 AGAGGUGUGCUCUGAACAA 57 1029 UUGUUCAGAGCACACCUCU 256 1029 AGCCGAGACGGGGCCGUGC 58 1029 AGCCGAGACGGGGCCGUGC 58 1047 GCACGGCCCCGUCUCGGCU 257 1047 CCGAGCAAUGAUCUCCCGC 59 1047 CCGAGCAAUGAUCUCCCGC 59 1065 GCGGGAGAUCAUUGCUCGG 258 1065 CUGGUACUUUGAUGUGACU 60 1065 CUGGUACUUUGAUGUGACU 60 1083 AGUCACAUCAAAGUACCAG 259 1083 UGAAGGGAAGUGUGCCCCA 61 1083 UGAAGGGAAGUGUGCCCCA 61 1101 UGGGGCACACUUCCCUUCA 260 1101 AUUCUUUUACGGCGGAUGU 62 1101 AUUCUUUUACGGCGGAUGU 62 1119 ACAUCCGCCGUAAAAGAAU 261 1119 UGGCGGCAACCGGAACAAC 63 1119 UGGCGGCAACCGGAACAAC 63 1137 GUUGUUCCGGUUGCCGCCA 262 1137 CUUUGACACAGAAGAGUAC 64 1137 CUUUGACACAGAAGAGUAC 64 1155 GUACUCUUCUGUGUCAAAG 263 1155 CUGCAUGGCCGUGUGUGGC 65 1155 CUGCAUGGCCGUGUGUGGC 65 1173 GCCACACACGGCCAUGCAG 264 1173 CAGCGCCAUGUCCCAAAGU 66 1173 CAGCGCCAUGUCCCAAAGU 66 1191 ACUUUGGGACAUGGCGCUG 265 1191 UUUACUCAAGACUACCCAG 67 1191 UUUACUCAAGACUACCCAG 67 1209 CUGGGUAGUCUUGAGUAAA 266 1209 GGAACCUCUUGCCCGAGAU 68 1209 GGAACCUCUUGCCCGAGAU 68 1227 AUCUCGGGCAAGAGGUUCC 267 1227 UCCUGUUAAACUUCCUACA 69 1227 UCCUGUUAAACUUCCUACA 69 1245 UGUAGGAAGUUUAACAGGA 268 1245 AACAGCAGCCAGUACCCCU 70 1245 AACAGCAGCCAGUACCCCU 70 1263 AGGGGUACUGGCUGCUGUU 269 1263 UGAUGCCGUUGACAAGUAU 71 1263 UGAUGCCGUUGACAAGUAU 71 1281 AUACUUGUCAACGGCAUCA 270 1281 UCUCGAGACACCUGGGGAU 72 1281 UCUCGAGACACCUGGGGAU 72 1299 AUCCCCAGGUGUCUCGAGA 271 1299 UGAGAAUGAACAUGCCCAU 73 1299 UGAGAAUGAACAUGCCCAU 73 1317 AUGGGCAUGUUCAUUCUCA 272 1317 UUUCCAGAAAGCCAAAGAG 74 1317 UUUCCAGAAAGCCAAAGAG 74 1335 CUCUUUGGCUUUCUGGAAA 273 1335 GAGGCUUGAGGCCAAGCAC 75 1335 GAGGCUUGAGGCCAAGCAC 75 1353 GUGCUUGGCCUCAAGCCUC 274 1353 CCGAGAGAGAAUGUCCCAG 76 1353 CCGAGAGAGAAUGUCCCAG 76 1371 CUGGGACAUUCUCUCUCGG 275 1371 GGUCAUGAGAGAAUGGGAA 77 1371 GGUCAUGAGAGAAUGGGAA 77 1389 UUCCCAUUCUCUCAUGACC 276 1389 AGAGGCAGAACGUCAAGCA 78 1389 AGAGGCAGAACGUCAAGCA 78 1407 UGCUUGACGUUCUGCCUCU 277 1407 AAAGAACUUGCCUAAAGCU 79 1407 AAAGAACUUGCCUAAAGCU 79 1425 AGCUUUAGGCAAGUUCUUU 278 1425 UGAUAAGAAGGCAGUUAUC 80 1425 UGAUAAGAAGGCAGUUAUC 80 1443 GAUAACUGCCUUCUUAUCA 279 1443 CCAGCAUUUCCAGGAGAAA 81 1443 CCAGCAUUUCCAGGAGAAA 81 1461 UUUCUCCUGGAAAUGCUGG 280 1461 AGUGGAAUCUUUGGAACAG 82 1461 AGUGGAAUCUUUGGAACAG 82 1479 CUGUUCCAAAGAUUCCACU 281 1479 GGAAGCAGCCAACGAGAGA 83 1479 GGAAGCAGCCAACGAGAGA 83 1497 UCUCUCGUUGGCUGCUUCC 282 1497 ACAGCAGCUGGUGGAGACA 84 1497 ACAGCAGGUGGUGGAGACA 84 1515 UGUCUCCACCAGCUGCUGU 283 1515 ACACAUGGCCAGAGUGGAA 85 1515 ACACAUGGCCAGAGUGGAA 85 1533 UUCCACUCUGGCCAUGUGU 284 1533 AGCCAUGCUCAAUGACCGC 86 1533 AGCCAUGCUCAAUGACCGC 86 1551 GCGGUCAUUGAGCAUGGCU 285 1551 CCGCCGCCUGGCCCUGGAG 87 1551 CCGCCGCCUGGCCCUGGAG 87 1569 CUCCAGGGCCAGGCGGCGG 286 1569 GAACUACAUCACCGCUCUG 88 1569 GAACUACAUCACCGCUCUG 88 1587 CAGAGCGGUGAUGUAGUUC 287 1587 GCAGGCUGUUCCUCCUCGG 89 1587 GCAGGCUGUUCCUCCUCGG 89 1605 CCGAGGAGGAACAGCCUGC 288 1605 GCCUCGUCACGUGUUCAAU 90 1605 GCCUCGUCACGUGUUCAAU 90 1623 AUUGAACACGUGACGAGGC 289 1623 UAUGCUAAAGAAGUAUGUC 91 1623 UAUGCUAAAGAAGUAUGUC 91 1641 GACAUACUUCUUUAGCAUA 290 1641 CCGCGCAGAACAGAAGGAC 92 1641 CCGCGCAGAACAGAAGGAC 92 1659 GUCCUUCUGUUCUGCGCGG 291 1659 CAGACAGCACACCCUAAAG 93 1659 CAGACAGCACACCCUAAAG 93 1677 CUUUAGGGUGUGCUGUCUG 292 1677 GCAUUUCGAGCAUGUGCGC 94 1677 GCAUUUCGAGCAUGUGCGC 94 1695 GCGCACAUGCUCGAAAUGC 293 1695 CAUGGUGGAUCCCAAGAAA 95 1695 CAUGGUGGAUCCCAAGAAA 95 1713 UUUCUUGGGAUCCACCAUG 294 1713 AGCCGCUCAGAUCCGGUCC 96 1713 AGCCGCUCAGAUCCGGUCC 96 1731 GGACCGGAUCUGAGCGGCU 295 1731 CCAGGUUAUGACACACCUC 97 1731 CCAGGUUAUGACACACCUC 97 1749 GAGGUGUGUCAUAACCUGG 296 1749 CCGUGUGAUUUAUGAGCGC 98 1749 CCGUGUGAUUUAUGAGCGC 98 1767 GCGCUCAUAAAUCACACGG 297 1767 CAUGAAUCAGUCUCUCUCC 99 1767 CAUGAAUCAGUCUCUCUCC 99 1785 GGAGAGAGACUGAUUCAUG 298 1785 CCUGCUCUACAACGUGCCU 100 1785 CCUGCUCUACAACGUGCCU 100 1803 AGGCACGUUGUAGAGCAGG 299 1803 UGCAGUGGCCGAGGAGAUU 101 1803 UGCAGUGGCCGAGGAGAUU 101 1821 AAUCUCCUCGGCCACUGCA 300 1821 UCAGGAUGAAGUUGAUGAG 102 1821 UCAGGAUGAAGUUGAUGAG 102 1839 CUCAUCAACUUCAUCCUGA 301 1839 GCUGCUUCAGAAAGAGCAA 103 1839 GCUGCUUCAGAAAGAGCAA 103 1857 UUGCUCUUUCUGAAGCAGC 302 1857 AAACUAUUCAGAUGACGUC 104 1857 AAACUAUUCAGAUGACGUC 104 1875 GACGUCAUCUGAAUAGUUU 303 1875 CUUGGCCAACAUGAUUAGU 105 1875 CUUGGCCAACAUGAUUAGU 105 1893 ACUAAUCAUGUUGGCCAAG 304 1893 UGAACCAAGGAUCAGUUAC 106 1893 UGAACCAAGGAUCAGUUAC 106 1911 GUAACUGAUCCUUGGUUCA 305 1911 CGGAAACGAUGCUCUCAUG 107 1911 CGGAAACGAUGCUCUCAUG 107 1929 CAUGAGAGCAUCGUUUCCG 306 1929 GCCAUCUUUGACCGAAACG 108 1929 GCCAUCUUUGACCGAAACG 108 1947 CGUUUCGGUCAAAGAUGGC 307 1947 GAAAACCACCGUGGAGCUC 109 1947 GAAAACCACCGUGGAGCUC 109 1965 GAGCUCCACGGUGGUUUUC 308 1965 CCUUCCCGUGAAUGGAGAG 110 1965 CCUUCCCGUGAAUGGAGAG 110 1983 CUCUCCAUUCACGGGAAGG 309 1983 GUUCAGCCUGGACGAUCUC 111 1983 GUUCAGCCUGGACGAUCUC 111 2001 GAGAUCGUCCAGGCUGAAC 310 2001 CCAGCCGUGGCAUUCUUUU 112 2001 CCAGCCGUGGCAUUCUUUU 112 2019 AAAAGAAUGCCACGGCUGG 311 2019 UGGGGCUGACUCUGUGCCA 113 2019 UGGGGCUGACUCUGUGCCA 113 2037 UGGCACAGAGUCAGCCCCA 312 2037 AGCCAACACAGAAAACGAA 114 2037 AGCCAACACAGAAAACGAA 114 2055 UUCGUUUUCUGUGUUGGCU 313 2055 AGUUGAGCCUGUUGAUGCC 115 2055 AGUUGAGCCUGUUGAUGCC 115 2073 GGCAUCAACAGGCUCAACU 314 2073 CCGCCCUGCUGCCGACCGA 116 2073 CCGCCCUGCUGCCGACCGA 116 2091 UCGGUCGGCAGCAGGGCGG 315 2091 AGGACUGACCACUCGACCA 117 2091 AGGACUGACCACUCGACCA 117 2109 UGGUCGAGUGGUCAGUCCU 316 2109 AGGUUCUGGGUUGACAAAU 118 2109 AGGUUCUGGGUUGACAAAU 118 2127 AUUUGUCAACCCAGAACCU 317 2127 UAUCAAGACGGAGGAGAUC 119 2127 UAUCAAGACGGAGGAGAUC 119 2145 GAUCUCCUCCGUCUUGAUA 318 2145 CUCUGAAGUGAAGAUGGAU 120 2145 CUCUGAAGUGAAGAUGGAU 120 2163 AUCCAUCUUCACUUCAGAG 319 2163 UGCAGAAUUCCGACAUGAC 121 2163 UGCAGAAUUCCGACAUGAC 121 2181 GUCAUGUCGGAAUUCUGCA 320 2181 CUCAGGAUAUGAAGUUCAU 122 2181 CUCAGGAUAUGAAGUUCAU 122 2199 AUGAACUUCAUAUCCUGAG 321 2199 UCAUCAAAAAUUGGUGUUC 123 2199 UCAUCAAAAAUUGGUGUUC 123 2217 GAACACCAAUUUUUGAUGA 322 2217 CUUUGCAGAAGAUGUGGGU 124 2217 CUUUGCAGAAGAUGUGGGU 124 2235 ACCCACAUCUUCUGCAAAG 323 2235 UUCAAACAAAGGUGCAAUC 125 2235 UUCAAACAAAGGUGCAAUC 125 2253 GAUUGCACCUUUGUUUGAA 324 2253 CAUUGGACUCAUGGUGGGC 126 2253 CAUUGGACUCAUGGUGGGC 126 2271 GCCCACCAUGAGUCCAAUG 325 2271 CGGUGUUGUCAUAGCGACA 127 2271 CGGUGUUGUCAUAGCGACA 127 2289 UGUCGCUAUGACAACACCG 326 2289 AGUGAUCGUCAUCACCUUG 128 2289 AGUGAUCGUCAUCACCUUG 128 2307 CAAGGUGAUGACGAUCACU 327 2307 GGUGAUGCUGAAGAAGAAA 129 2307 GGUGAUGCUGAAGAAGAAA 129 2325 UUUCUUCUUCAGCAUCACC 328 2325 ACAGUACACAUCCAUUCAU 130 2325 ACAGUACACAUCCAUUCAU 130 2343 AUGAAUGGAUGUGUACUGU 329 2343 UCAUGGUGUGGUGGAGGUU 131 2343 UCAUGGUGUGGUGGAGGUU 131 2361 AACCUCCACCACACCAUGA 330 2361 UGACGCCGCUGUCACCCCA 132 2361 UGACGCCGCUGUCACCCCA 132 2379 UGGGGUGACAGCGGCGUCA 331 2379 AGAGGAGCGCCACCUGUCC 133 2379 AGAGGAGCGCCACCUGUCC 133 2397 GGACAGGUGGCGCUCCUCU 332 2397 CAAGAUGCAGCAGAACGGC 134 2397 CAAGAUGCAGCAGAACGGC 134 2415 GCCGUUCUGCUGCAUCUUG 333 2415 CUACGAAAAUCCAACCUAC 135 2415 CUACGAAAAUCCAACCUAC 135 2433 GUAGGUUGGAUUUUCGUAG 334 2433 CAAGUUCUUUGAGCAGAUG 136 2433 CAAGUUCUUUGAGCAGAUG 136 2451 CAUCUGCUCAAAGAACUUG 335 2451 GCAGAACUAGACCCCCGCC 137 2451 GCAGAACUAGACCCCCGCC 137 2469 GGCGGGGGUCUAGUUCUGC 336 2469 CACAGCAGCCUCUGAAGUU 138 2469 CACAGCAGCCUCUGAAGUU 138 2487 AACUUCAGAGGCUGCUGUG 337 2487 UGGACAGCAAAACCAUUGC 139 2487 UGGACAGCAAAACCAUUGC 139 2505 GCAAUGGUUUUGCUGUCCA 338 2505 CUUCACUACCCAUCGGUGU 140 2505 CUUCACUACCCAUCGGUGU 140 2523 ACACCGAUGGGUAGUGAAG 339 2523 UCCAUUUAUAGAAUAAUGU 141 2523 UCCAUUUAUAGAAUAAUGU 141 2541 ACAUUAUUCUAUAAAUGGA 340 2541 UGGGAAGAAACAAACCCGU 142 2541 UGGGAAGAAACAAACCCGU 142 2559 ACGGGUUUGUUUCUUCCCA 341 2559 UUUUAUGAUUUACUCAUUA 143 2559 UUUUAUGAUUUACUCAUUA 143 2577 UAAUGAGUAAAUCAUAAAA 342 2577 AUCGCCUUUUGACAGCUGU 144 2577 AUCGCCUUUUGACAGCUGU 144 2595 ACAGCUGUCAAAAGGCGAU 343 2595 UGCUGUAACACAAGUAGAU 145 2595 UGCUGUAACACAAGUAGAU 145 2613 AUCUACUUGUGUUACAGCA 344 2613 UGCCUGAACUUGAAUUAAU 146 2613 UGCCUGAACUUGAAUUAAU 146 2631 AUUAAUUCAAGUUCAGGCA 345 2631 UCCACACAUCAGUAAUGUA 147 2631 UCCACACAUCAGUAAUGUA 147 2649 UACAUUACUGAUGUGUGGA 346 2649 AUUCUAUCUCUCUUUACAU 148 2649 AUUCUAUCUCUCUUUACAU 148 2667 AUGUAAAGAGAGAUAGAAU 347 2667 UUUUGGUCUCUAUACUACA 149 2667 UUUUGGUCUCUAUACUACA 149 2685 UGUAGUAUAGAGACCAAAA 348 2685 AUUAUUAAUGGGUUUUGUG 150 2685 AUUAUUAAUGGGUUUUGUG 150 2703 CACAAAACCCAUUAAUAAU 349 2703 GUACUGUAAAGAAUUUAGC 151 2703 GUACUGUAAAGAAUUUAGC 151 2721 GCUAAAUUCUUUACAGUAC 350 2721 CUGUAUCAAACUAGUGCAU 152 2721 CUGUAUCAAACUAGUGCAU 152 2739 AUGCACUAGUUUGAUACAG 351 2739 UGAAUAGAUUCUCUCCUGA 153 2739 UGAAUAGAUUCUCUCCUGA 153 2757 UCAGGAGAGAAUCUAUUCA 352 2757 AUUAUUUAUCACAUAGCCC 154 2757 AUUAUUUAUCACAUAGCCC 154 2775 GGGCUAUGUGAUAAAUAAU 353 2775 CCUUAGCCAGUUGUAUAUU 155 2775 CCUUAGCCAGUUGUAUAUU 155 2793 AAUAUACAACUGGCUAAGG 354 2793 UAUUCUUGUGGUUUGUGAC 156 2793 UAUUCUUGUGGUUUGUGAC 156 2811 GUCACAAACCACAAGAAUA 355 2811 CCCAAUUAAGUCCUACUUU 157 2811 CCCAAUUAAGUCCUACUUU 157 2829 AAAGUAGGACUUAAUUGGG 356 2829 UACAUAUGCUUUAAGAAUC 158 2829 UACAUAUGCUUUAAGAAUC 158 2847 GAUUCUUAAAGCAUAUGUA 357 2847 CGAUGGGGGAUGCUUCAUG 159 2847 CGAUGGGGGAUGCUUCAUG 159 2865 CAUGAAGCAUCCCCCAUCG 358 2865 GUGAACGUGGGAGUUCAGC 160 2865 GUGAACGUGGGAGUUCAGC 160 2883 GCUGAACUCCCACGUUCAC 359 2883 CUGCUUCUCUUGCCUAAGU 161 2883 CUGCUUCUCUUGCCUAAGU 161 2901 ACUUAGGCAAGAGAAGCAG 360 2901 UAUUCCUUUCCUGAUCACU 162 2901 UAUUCCUUUCCUGAUCACU 162 2919 AGUGAUCAGGAAAGGAAUA 361 2919 UAUGCAUUUUAAAGUUAAA 163 2919 UAUGCAUUUUAAAGUUAAA 163 2937 UUUAACUUUAAAAUGCAUA 362 2937 ACAUUUUUAAGUAUUUCAG 164 2937 ACAUUUUUAAGUAUUUCAG 164 2955 CUGAAAUACUUAAAAAUGU 363 2955 GAUGCUUUAGAGAGAUUUU 165 2955 GAUGCUUUAGAGAGAUUUU 165 2973 AAAAUCUCUCUAAAGCAUC 384 2973 UUUUUCCAUGACUGCAUUU 166 2973 UUUUUCCAUGACUGCAUUU 166 2991 AAAUGCAGUCAUGGAAAAA 365 2991 UUACUGUACAGAUUGCUGC 167 2991 UUACUGUACAGAUUGCUGC 167 3009 GCAGCAAUCUGUACAGUAA 366 3009 CUUCUGCUAUAUUUGUGAU 168 3009 CUUCUGCUAUAUUUGUGAU 168 3027 AUCACAAAUAUAGCAGAAG 367 3027 UAUAGGAAUUAAGAGGAUA 169 3027 UAUAGGAAUUAAGAGGAUA 169 3045 UAUCCUCUUAAUUCCUAUA 368 3045 ACACACGUUUGUUUCUUCG 170 3045 ACACACGUUUGUUUCUUCG 170 3063 CGAAGAAACAAACGUGUGU 369 3063 GUGCCUGUUUUAUGUGCAC 171 3063 GUGCCUGUUUUAUGUGCAC 171 3081 GUGCACAUAAAACAGGCAC 370 3081 CACAUUAGGCAUUGAGACU 172 3081 CACAUUAGGCAUUGAGACU 172 3099 AGUCUCAAUGCCUAAUGUG 371 3099 UUCAAGCUUUUCUUUUUUU 173 3099 UUCAAGCUUUUCUUUUUUU 173 3117 AAAAAAAGAAAAGCUUGAA 372 3117 UGUCCACGUAUCUUUGGGU 174 3117 UGUCCACGUAUCUUUGGGU 174 3135 ACCCAAAGAUACGUGGACA 373 3135 UCUUUGAUAAAGAAAAGAA 175 3135 UCUUUGAUAAAGAAAAGAA 175 3153 UUCUUUUCUUUAUCAAAGA 374 3153 AUCCCUGUUCAUUGUAAGC 176 3153 AUCCCUGUUCAUUGUAAGC 176 3171 GCUUACAAUGAACAGGGAU 375 3171 CACUUUUACGGGGCGGGUG 177 3171 CACUUUUACGGGGCGGGUG 177 3189 CACCCGCCCCGUAAAAGUG 376 3189 GGGGAGGGGUGCUCUGCUG 178 3189 GGGGAGGGGUGCUCUGCUG 178 3207 CAGCAGAGCACCCCUCCCC 377 3207 GGUCUUCAAUUACCAAGAA 179 3207 GGUCUUCAAUUACCAAGAA 179 3225 UUCUUGGUAAUUGAAGACC 378 3225 AUUCUCCAAAACAAUUUUC 180 3225 AUUCUCCAAAACAAUUUUC 180 3243 GAAAAUUGUUUUGGAGAAU 379 3243 CUGCAGGAUGAUUGUACAG 181 3243 CUGCAGGAUGAUUGUACAG 181 3261 CUGUACAAUCAUCCUGCAG 380 3261 GAAUCAUUGCUUAUGACAU 182 3261 GAAUCAUUGCUUAUGACAU 182 3279 AUGUCAUAAGCAAUGAUUC 381 3279 UGAUCGCUUUCUACACUGU 183 3279 UGAUCGCUUUCUACACUGU 183 3297 ACAGUGUAGAAAGCGAUCA 382 3297 UAUUACAUAAAUAAAUUAA 184 3297 UAUUACAUAAAUAAAUUAA 184 3315 UUAAUUUAUUUAUGUAAUA 383 3315 AAUAAAAUAACCCCGGGCA 185 3315 AAUAAAAUAACCCCGGGCA 185 3333 UGCCCGGGGUUAUUUUAUU 384 3333 AAGACUUUUCUUUGAAGGA 186 3333 AAGACUUUUCUUUGAAGGA 186 3351 UCCUUCAAAGAAAAGUCUU 385 3351 AUGACUACAGACAUUAAAU 187 3351 AUGACUACAGACAUUAAAU 187 3369 AUUUAAUGUCUGUAGUCAU 386 3369 UAAUCGAAGUAAUUUUGGG 188 3369 UAAUCGAAGUAAUUUUGGG 188 3387 CCCAAAAUUACUUCGAUUA 387 3387 GUGGGGAGAAGAGGCAGAU 189 3387 GUGGGGAGAAGAGGCAGAU 189 3405 AUCUGCCUCUUCUCCCCAC 388 3405 UUCAAUUUUCUUUAACCAG 190 3405 UUCAAUUUUCUUUAACCAG 190 3423 CUGGUUAAAGAAAAUUGAA 389 3423 GUCUGAAGUUUCAUUUAUG 191 3423 GUCUGAAGUUUCAUUUAUG 191 3441 CAUAAAUGAAACUUCAGAC 390 3441 GAUACAAAAGAAGAUGAAA 192 3441 GAUACAAAAGAAGAUGAAA 192 3459 UUUCAUCUUCUUUUGUAUC 391 3459 AAUGGAAGUGGCAAUAUAA 193 3459 AAUGGAAGUGGCAAUAUAA 193 3477 UUAUAUUGCCACUUCCAUU 392 3477 AGGGGAUGAGGAAGGCAUG 194 3477 AGGGGAUGAGGAAGGCAUG 194 3495 CAUGCCUUCCUCAUCCCCU 393 3495 GCCUGGACAAACCCUUCUU 195 3495 GCCUGGACAAACCCUUCUU 195 3513 AAGAAGGGUUUGUCCAGGC 394 3513 UUUAAGAUGUGUCUUCAAU 196 3513 UUUAAGAUGUGUCUUCAAU 196 3531 AUUGAAGACACAUCUUAAA 395 3531 UUUGUAUAAAAUGGUGUUU 197 3531 UUUGUAUAAAAUGGUGUUU 197 3549 AAACACCAUUUUAUACAAA 396 3549 UUCAUGUAAAUAAAUACAU 198 3549 UUCAUGUAAAUAAAUACAU 198 3567 AUGUAUUUAUUUACAUGAA 397 3559 UAAAUACAUUCUUGGAGGA 199 3559 UAAAUACAUUCUUGGAGGA 199 3577 UCCUCCAAGAAUGUAUUUA 398 BACE NM_012104 Seq Seq Seq Pos Seq ID UPos Upper seq ID LPos Lower seq ID 1 CGCACUCGUCCCCAGCCCG 399 1 CGCACUCGUCCCCAGCCCG 399 19 CGGGCUGGGGACGAGUGCG 724 19 GCCCGGGAGCUGCGAGCCG 400 19 GCCCGGGAGCUGCGAGCCG 400 37 CGGCUCGCAGCUCCCGGGC 725 37 GCGAGCUGGAUUAUGGUGG 401 37 GCGAGCUGGAUUAUGGUGG 401 55 CCACCAUAAUCCAGCUCGC 726 55 GCCUGAGCAGCCAACGCAG 402 55 GCCUGAGCAGCCAACGCAG 402 73 CUGCGUUGGCUGCUCAGGC 727 73 GCCGCAGGAGCCCGGAGCC 403 73 GCCGCAGGAGCCCGGAGCC 403 91 GGCUCCGGGCUCCUGCGGC 728 91 CCUUGCCCCUGCCCGCGCC 404 91 CCUUGCCCCUGCCCGCGCC 404 109 GGCGCGGGCAGGGGCAAGG 729 109 CGCCGCCCGCCGGGGGGAC 405 109 CGCCGCCCGCCGGGGGGAC 405 127 GUCCCCCCGGCGGGCGGCG 730 127 CCAGGGAAGCCGCCACCGG 406 127 CCAGGGAAGCCGCCACCGG 406 145 CCGGUGGCGGCUUCCCUGG 731 145 GCCCGCCAUGCCCGCCCCU 407 145 GCCCGCCAUGCCCGCCCCU 407 163 AGGGGCGGGCAUGGCGGGC 732 163 UCCCAGCCCCGCCGGGAGC 408 163 UCCCAGCCCCGCCGGGAGC 408 181 GCUCCCGGCGGGGCUGGGA 733 181 CCCGCGCCCGCUGCCCAGG 409 181 CCCGCGCCCGCUGCCCAGG 409 199 CCUGGGCAGCGGGCGCGGG 734 199 GCUGGCCGCCGCCGUGCCG 410 199 GCUGGCCGCCGCCGUGCCG 410 217 CGGCACGGCGGCGGCCAGC 735 217 GAUGUAGCGGGCUCCGGAU 411 217 GAUGUAGCGGGCUCCGGAU 411 235 AUCCGGAGCCCGCUACAUC 736 235 UCCCAGCCUCUCCCCUGCU 412 235 UCCCAGCCUCUCCCCUGCU 412 253 AGCAGGGGAGAGGCUGGGA 737 253 UCCCGUGCUCUGCGGAUCU 413 253 UCCCGUGCUCUGCGGAUCU 413 271 AGAUCCGCAGAGCACGGGA 738 271 UCCCCUGACCGCUCUCCAC 414 271 UCCCCUGACCGCUCUCCAC 414 289 GUGGAGAGCGGUCAGGGGA 739 289 CAGCCCGGACCCGGGGGCU 415 289 CAGCCCGGACCCGGGGGCU 415 307 AGCCCCCGGGUCCGGGCUG 740 307 UGGCCCAGGGCCCUGCAGG 416 307 UGGCCCAGGGCCCUGCAGG 416 325 CCUGCAGGGCCCUGGGCCA 741 325 GCCCUGGCGUCCUGAUGCC 417 325 GCCCUGGCGUCCUGAUGCC 417 343 GGCAUCAGGACGCCAGGGC 742 343 CCCCAAGCUCCCUCUCCUG 418 343 CCCCAAGCUCCCUCUCCUG 418 361 CAGGAGAGGGAGCUUGGGG 743 361 GAGAAGCCACCAGCACCAC 419 361 GAGAAGCCACCAGCACCAC 419 379 GUGGUGCUGGUGGCUUCUC 744 379 CCCAGACUUGGGGGCAGGC 420 379 CCCAGACUUGGGGGCAGGC 420 397 GCCUGCCCCCAAGUCUGGG 745 397 CGCCAGGGACGGACGUGGG 421 397 CGCCAGGGACGGACGUGGG 421 415 CCCACGUCCGUCCCUGGCG 746 415 GCCAGUGCGAGCCCAGAGG 422 415 GCCAGUGCGAGCCCAGAGG 422 433 CCUCUGGGCUCGCACUGGC 747 433 GGCCCGAAGGCCGGGGCCC 423 433 GGCCCGAAGGCCGGGGCCC 423 451 GGGCCCCGGCCUUCGGGCC 748 451 CACCAUGGCCCAAGCCCUG 424 451 CACCAUGGCCCAAGCCCUG 424 469 CAGGGCUUGGGCCAUGGUG 749 469 GCCCUGGCUCCUGCUGUGG 425 469 GCCCUGGCUCCUGCUGUGG 425 487 CCACAGCAGGAGCCAGGGC 750 487 GAUGGGCGCGGGAGUGCUG 426 487 GAUGGGCGCGGGAGUGCUG 426 505 CAGCACUCCCGCGCCCAUC 751 505 GCCUGCCCACGGCACCCAG 427 505 GCCUGCCCACGGCACCCAG 427 523 CUGGGUGCCGUGGGCAGGC 752 523 GCACGGCAUCCGGCUGCCC 428 523 GCACGGCAUCCGGCUGCCC 428 541 GGGCAGCCGGAUGCCGUGC 753 541 CCUGCGCAGCGGCCUGGGG 429 541 CCUGCGCAGCGGCCUGGGG 429 559 CCCCAGGCCGCUGCGCAGG 754 559 GGGCGCCCCCCUGGGGCUG 430 559 GGGCGCCCCCCUGGGGCUG 430 577 CAGCCCCAGGGGGGCGCCC 755 577 GCGGCUGCCCCGGGAGACC 431 577 GCGGCUGCCCCGGGAGACC 431 595 GGUCUCCCGGGGCAGCCGC 756 595 CGACGAAGAGCCCGAGGAG 432 595 CGACGAAGAGCCCGAGGAG 432 613 CUCCUCGGGCUCUUCGUCG 757 613 GCCCGGCCGGAGGGGCAGC 433 613 GCCCGGCCGGAGGGGCAGC 433 631 GCUGCCCCUCCGGCCGGGC 758 631 CUUUGUGGAGAUGGUGGAC 434 631 CUUUGUGGAGAUGGUGGAC 434 649 GUCCACCAUCUCCACAAAG 759 649 CAACCUGAGGGGCAAGUCG 435 649 CAACCUGAGGGGCAAGUCG 435 667 CGACUUGCCCCUCAGGUUG 760 667 GGGGCAGGGCUACUACGUG 436 667 GGGGCAGGGCUACUACGUG 436 685 CACGUAGUAGCCCUGCCCC 761 685 GGAGAUGACCGUGGGCAGC 437 685 GGAGAUGACCGUGGGCAGC 437 703 GCUGCCCACGGUCAUCUCC 762 703 CCCCCCGCAGACGCUCAAC 438 703 CCCCCCGCAGACGCUCAAC 438 721 GUUGAGCGUCUGCGGGGGG 763 721 CAUCCUGGUGGAUACAGGC 439 721 CAUCCUGGUGGAUACAGGC 439 739 GCCUGUAUCCACCAGGAUG 764 739 CAGCAGUAACUUUGCAGUG 440 739 CAGCAGUAACUUUGCAGUG 440 757 CACUGCAAAGUUACUGCUG 765 757 GGGUGCUGCCCCCCACCCC 441 757 GGGUGCUGCCCCCCACCCC 441 775 GGGGUGGGGGGCAGCACCC 766 775 CUUCCUGCAUCGCUACUAC 442 775 CUUCCUGCAUCGCUACUAC 442 793 GUAGUAGCGAUGCAGGAAG 767 793 CCAGAGGCAGCUGUCCAGC 443 793 CCAGAGGCAGCUGUCCAGC 443 811 GCUGGACAGCUGCCUCUGG 768 811 CACAUACCGGGACCUCCGG 444 811 CACAUACCGGGACCUCCGG 444 829 CCGGAGGUCCCGGUAUGUG 769 829 GAAGGGUGUGUAUGUGCCC 445 829 GAAGGGUGUGUAUGUGCCC 445 847 GGGCACAUACACACCCUUC 770 847 CUACACCCAGGGCAAGUGG 446 847 CUACACCCAGGGCAAGUGG 446 865 CCACUUGCCCUGGGUGUAG 771 865 GGAAGGGGAGCUGGGCACC 447 865 GGAAGGGGAGCUGGGCACC 447 883 GGUGCCCAGCUCCCCUUCC 772 883 CGACCUGGUAAGCAUCCCC 448 883 CGACCUGGUAAGCAUCCCC 448 901 GGGGAUGCUUACCAGGUCG 773 901 CCAUGGCCCCAACGUCACU 449 901 CCAUGGCCCCAACGUCACU 449 919 AGUGACGUUGGGGCCAUGG 774 919 UGUGCGUGCCAACAUUGCU 450 919 UGUGCGUGCCAACAUUGCU 450 937 AGCAAUGUUGGCACGCACA 775 937 UGCCAUCACUGAAUCAGAC 451 937 UGCCAUCACUGAAUCAGAC 451 955 GUCUGAUUCAGUGAUGGCA 776 955 CAAGUUCUUCAUCAACGGC 452 955 CAAGUUCUUCAUCAACGGC 452 973 GCCGUUGAUGAAGAACUUG 777 973 CUCCAACUGGGAAGGCAUC 453 973 CUCCAACUGGGAAGGCAUC 453 991 GAUGCCUUCCCAGUUGGAG 778 991 CCUGGGGCUGGCCUAUGCU 454 991 CCUGGGGCUGGCCUAUGCU 454 1009 AGCAUAGGCCAGCCCCAGG 779 1009 UGAGAUUGCCAGGCCUGAC 455 1009 UGAGAUUGCCAGGCCUGAC 455 1027 GUCAGGCCUGGCAAUCUCA 780 1027 CGACUCCCUGGAGCCUUUC 456 1027 CGACUCCCUGGAGCCUUUC 456 1045 GAAAGGCUCCAGGGAGUCG 781 1045 CUUUGACUCUCUGGUAAAG 457 1045 CUUUGACUCUCUGGUAAAG 457 1063 CUUUACCAGAGAGUCAAAG 782 1063 GCAGACCCACGUUCCCAAC 458 1063 GCAGACCCACGUUCCCAAC 458 1081 GUUGGGAACGUGGGUCUGC 783 1081 CCUCUUCUCCCUGCAGCUU 459 1081 CCUCUUCUCCCUGCAGCUU 459 1099 AAGCUGCAGGGAGAAGAGG 784 1099 UUGUGGUGCUGGCUUCCCC 460 1099 UUGUGGUGCUGGCUUCCCC 460 1117 GGGGAAGCCAGCACCACAA 785 1117 CCUCAACCAGUCUGAAGUG 461 1117 CCUCAACCAGUCUGAAGUG 461 1135 CACUUCAGACUGGUUGAGG 786 1135 GCUGGCCUCUGUCGGAGGG 462 1135 GCUGGCCUCUGUCGGAGGG 462 1153 CCCUCCGACAGAGGCCAGC 787 1153 GAGCAUGAUCAUUGGAGGU 463 1153 GAGCAUGAUCAUUGGAGGU 463 1171 ACCUCCAAUGAUCAUGCUC 788 1171 UAUCGACCACUCGCUGUAC 464 1171 UAUCGACCACUCGCUGUAC 464 1189 GUACAGCGAGUGGUCGAUA 789 1189 CACAGGCAGUCUCUGGUAU 465 1189 CACAGGCAGUCUCUGGUAU 465 1207 AUACCAGAGACUGCCUGUG 790 1207 UACACCCAUCCGGCGGGAG 466 1207 UACACCCAUCCGGCGGGAG 466 1225 CUCCCGCCGGAUGGGUGUA 791 1225 GUGGUAUUAUGAGGUCAUC 467 1225 GUGGUAUUAUGAGGUCAUC 467 1243 GAUGACCUCAUAAUACCAC 792 1243 CAUUGUGCGGGUGGAGAUC 468 1243 CAUUGUGCGGGUGGAGAUC 468 1261 GAUCUCCACCCGCACAAUG 793 1261 CAAUGGACAGGAUCUGAAA 469 1261 CAAUGGACAGGAUCUGAAA 469 1279 UUUCAGAUCCUGUCCAUUG 794 1279 AAUGGACUGCAAGGAGUAC 470 1279 AAUGGACUGCAAGGAGUAC 470 1297 GUACUCCUUGCAGUCCAUU 795 1297 CAACUAUGACAAGAGCAUU 471 1297 CAACUAUGACAAGAGCAUU 471 1315 AAUGCUCUUGUCAUAGUUG 796 1315 UGUGGACAGUGGCACCACC 472 1315 UGUGGACAGUGGCACCACC 472 1333 GGUGGUGCCACUGUCCACA 797 1333 CAACCUUCGUUUGCCCAAG 473 1333 CAACCUUCGUUUGCCCAAG 473 1351 CUUGGGCAAACGAAGGUUG 798 1351 GAAAGUGUUUGAAGCUGCA 474 1351 GAAAGUGUUUGAAGCUGCA 474 1369 UGCAGCUUCAAACACUUUC 799 1369 AGUCAAAUCCAUCAAGGCA 475 1369 AGUCAAAUCCAUCAAGGCA 475 1387 UGCCUUGAUGGAUUUGACU 800 1387 AGCCUCCUCCACGGAGAAG 476 1387 AGCCUCCUCCACGGAGAAG 476 1405 CUUCUCCGUGGAGGAGGCU 801 1405 GUUCCCUGAUGGUUUCUGG 477 1405 GUUCCCUGAUGGUUUCUGG 477 1423 CCAGAAACCAUCAGGGAAC 802 1423 GCUAGGAGAGCAGCUGGUG 478 1423 GCUAGGAGAGCAGCUGGUG 478 1441 CACCAGCUGCUCUCCUAGC 803 1441 GUGCUGGCAAGCAGGCACC 479 1441 GUGCUGGCAAGCAGGCACC 479 1459 GGUGCCUGCUUGCCAGCAC 804 1459 CACCCCUUGGAACAUUUUC 480 1459 CACCCCUUGGAACAUUUUC 480 1477 GAAAAUGUUCCAAGGGGUG 805 1477 CCCAGUCAUCUCACUCUAC 481 1477 CCCAGUCAUCUCACUCUAC 481 1495 GUAGAGUGAGAUGACUGGG 806 1495 CCUAAUGGGUGAGGUUACC 482 1495 CCUAAUGGGUGAGGUUACC 482 1513 GGUAACCUCACCCAUUAGG 807 1513 CAACCAGUCCUUCCGCAUC 483 1513 CAACCAGUCCUUCCGCAUC 483 1531 GAUGCGGAAGGACUGGUUG 808 1531 CACCAUCCUUCCGCAGCAA 484 1531 CACCAUCCUUCCGCAGCAA 484 1549 UUGCUGCGGAAGGAUGGUG 809 1549 AUACCUGCGGCCAGUGGAA 485 1549 AUACCUGCGGCCAGUGGAA 485 1567 UUCCACUGGCCGCAGGUAU 810 1567 AGAUGUGGCCACGUCCCAA 486 1567 AGAUGUGGCCACGUCCCAA 486 1585 UUGGGACGUGGCCACAUCU 811 1585 AGACGACUGUUACAAGUUU 487 1585 AGACGACUGUUACAAGUUU 487 1603 AAACUUGUAACAGUCGUCU 812 1603 UGCCAUCUCACAGUCAUCC 488 1603 UGCCAUCUCACAGUCAUCC 488 1621 GGAUGACUGUGAGAUGGCA 813 1621 CACGGGCACUGUUAUGGGA 489 1621 CACGGGCACUGUUAUGGGA 489 1639 UCCCAUAACAGUGCCCGUG 814 1639 AGCUGUUAUCAUGGAGGGC 490 1639 AGCUGUUAUCAUGGAGGGC 490 1657 GCCCUCCAUGAUAACAGCU 815 1657 CUUCUACGUUGUCUUUGAU 491 1657 CUUCUACGUUGUCUUUGAU 491 1675 AUCAAAGACAACGUAGAAG 816 1675 UCGGGCCCGAAAACGAAUU 492 1675 UCGGGCCCGAAAACGAAUU 492 1693 AAUUCGUUUUCGGGCCCGA 817 1693 UGGCUUUGCUGUCAGCGCU 493 1693 UGGCUUUGCUGUCAGCGCU 493 1711 AGCGCUGACAGCAAAGCCA 818 1711 UUGCCAUGUGCACGAUGAG 494 1711 UUGCCAUGUGCACGAUGAG 494 1729 CUCAUCGUGCACAUGGCAA 819 1729 GUUCAGGACGGCAGCGGUG 495 1729 GUUCAGGACGGCAGCGGUG 495 1747 CACCGCUGCCGUCCUGAAC 820 1747 GGAAGGCCCUUUUGUCACC 496 1747 GGAAGGCCCUUUUGUCACC 496 1765 GGUGACAAAAGGGCCUUCC 821 1765 CUUGGACAUGGAAGACUGU 497 1765 CUUGGACAUGGAAGACUGU 497 1783 ACAGUCUUCCAUGUCCAAG 822 1783 UGGCUACAACAUUCCACAG 498 1783 UGGCUACAACAUUCCACAG 498 1801 CUGUGGAAUGUUGUAGCCA 823 1801 GACAGAUGAGUCAACCCUC 499 1801 GACAGAUGAGUCAACCCUC 499 1819 GAGGGUUGACUCAUCUGUC 824 1819 CAUGACCAUAGCCUAUGUC 500 1819 CAUGACCAUAGCCUAUGUC 500 1837 GACAUAGGCUAUGGUCAUG 825 1837 CAUGGCUGCCAUCUGCGCC 501 1837 CAUGGCUGCCAUCUGCGCC 501 1855 GGCGCAGAUGGCAGCCAUG 826 1855 CCUCUUCAUGCUGCCACUC 502 1855 CCUCUUCAUGCUGCCACUC 502 1873 GAGUGGCAGCAUGAAGAGG 827 1873 CUGCCUCAUGGUGUGUCAG 503 1873 CUGCCUCAUGGUGUGUCAG 503 1891 CUGACACACCAUGAGGCAG 828 1891 GUGGCGCUGCCUCCGCUGC 504 1891 GUGGCGCUGCCUCCGCUGC 504 1909 GCAGCGGAGGCAGCGCCAC 829 1909 CCUGCGCCAGCAGCAUGAU 505 1909 CCUGCGCCAGCAGCAUGAU 505 1927 AUCAUGCUGCUGGCGCAGG 830 1927 UGACUUUGCUGAUGACAUC 506 1927 UGACUUUGCUGAUGACAUC 506 1945 GAUGUCAUCAGCAAAGUCA 831 1945 CUCCCUGCUGAAGUGAGGA 507 1945 CUCCCUGCUGAAGUGAGGA 507 1963 UCCUCACUUCAGCAGGGAG 832 1953 AGGCCCAUGGGCAGAAGAU 508 1963 AGGCCCAUGGGCAGAAGAU 508 1981 AUCUUCUGCCCAUGGGCCU 833 1981 UAGAGAUUCCCCUGGACCA 509 1981 UAGAGAUUCCCCUGGACCA 509 1999 UGGUCCAGGGGAAUCUCUA 834 1999 ACACCUCCGUGGUUCACUU 510 1999 ACACCUCCGUGGUUCACUU 510 2017 AAGUGAACCACGGAGGUGU 835 2017 UUGGUCACAAGUAGGAGAC 511 2017 UUGGUCACAAGUAGGAGAC 511 2035 GUCUCCUACUUGUGACCAA 836 2035 CACAGAUGGCACCUGUGGC 512 2035 CACAGAUGGCACCUGUGGC 512 2053 GCCACAGGUGCCAUCUGUG 837 2053 CCAGAGCACCUCAGGACCC 513 2053 CCAGAGCACCUCAGGACCC 513 2071 GGGUCCUGAGGUGCUCUGG 838 2071 CUCCCCACCCACCAAAUGC 514 2071 CUCCCCACCCACCAAAUGC 514 2089 GCAUUUGGUGGGUGGGGAG 839 2089 CCUCUGCCUUGAUGGAGAA 515 2089 CCUCUGCCUUGAUGGAGAA 515 2107 UUCUCCAUCAAGGCAGAGG 840 2107 AGGAAAAGGCUGGCAAGGU 516 2107 AGGAAAAGGCUGGCAAGGU 516 2125 ACCUUGCCAGCCUUUUCCU 841 2125 UGGGUUCCAGGGACUGUAC 517 2125 UGGGUUCCAGGGACUGUAC 517 2143 GUACAGUCCCUGGAACCCA 842 2143 CCUGUAGGAAACAGAAAAG 518 2143 CCUGUAGGAAACAGAAAAG 518 2161 CUUUUCUGUUUCCUACAGG 843 2161 GAGAAGAAAGAAGCACUCU 519 2161 GAGAAGAAAGAAGCACUCU 519 2179 AGAGUGCUUCUUUCUUCUC 844 2179 UGCUGGCGGGAAUACUCUU 520 2179 UGCUGGCGGGAAUACUCUU 520 2197 AAGAGUAUUCCCGCCAGCA 845 2197 UGGUCACCUCAAAUUUAAG 521 2197 UGGUCACCUCAAAUUUAAG 521 2215 CUUAAAUUUGAGGUGACCA 846 2215 GUCGGGAAAUUCUGCUGCU 522 2215 GUCGGGAAAUUCUGCUGCU 522 2233 AGCAGCAGAAUUUCCCGAC 847 2233 UUGAAACUUCAGCCCUGAA 523 2233 UUGAAACUUCAGCCCUGAA 523 2251 UUCAGGGCUGAAGUUUCAA 848 2251 ACCUUUGUCCACCAUUCCU 524 2251 ACCUUUGUCCACCAUUCCU 524 2269 AGGAAUGGUGGACAAAGGU 849 2269 UUUAAAUUCUCCAACCCAA 525 2269 UUUAAAUUCUCCAACCCAA 525 2287 UUGGGUUGGAGAAUUUAAA 850 2287 AAGUAUUCUUCUUUUCUUA 526 2287 AAGUAUUCUUCUUUUCUUA 526 2305 UAAGAAAAGAAGAAUACUU 851 2305 AGUUUCAGAAGUACUGGCA 527 2305 AGUUUCAGAAGUACUGGCA 527 2323 UGCCAGUACUUCUGAAACU 852 2323 AUCACACGCAGGUUACCUU 528 2323 AUCACACGCAGGUUACCUU 528 2341 AAGGUAACCUGCGUGUGAU 853 2341 UGGCGUGUGUCCCUGUGGU 529 2341 UGGCGUGUGUCCCUGUGGU 529 2359 ACCACAGGGACACACGCCA 854 2359 UACCCUGGCAGAGAAGAGA 530 2359 UACCCUGGCAGAGAAGAGA 530 2377 UCUCUUCUCUGCCAGGGUA 855 2377 ACCAAGCUUGUUUCCCUGC 531 2377 ACCAAGCUUGUUUCCCUGC 531 2395 GCAGGGAAACAAGCUUGGU 856 2395 CUGGCCAAAGUCAGUAGGA 532 2395 CUGGCCAAAGUCAGUAGGA 532 2413 UCCUACUGACUUUGGCCAG 857 2413 AGAGGAUGCACAGUUUGCU 533 2413 AGAGGAUGCACAGUUUGCU 533 2431 AGCAAACUGUGCAUCCUCU 858 2431 UAUUUGCUUUAGAGACAGG 534 2431 UAUUUGCUUUAGAGACAGG 534 2449 CCUGUCUCUAAAGCAAAUA 859 2449 GGACUGUAUAAACAAGCCU 535 2449 GGACUGUAUAAACAAGCCU 535 2467 AGGCUUGUUUAUACAGUCC 860 2467 UAACAUUGGUGCAAAGAUU 536 2467 UAACAUUGGUGCAAAGAUU 536 2485 AAUCUUUGCACCAAUGUUA 861 2485 UGCCUCUUGAAUUAAAAAA 537 2485 UGCCUCUUGAAUUAAAAAA 537 2503 UUUUUUAAUUCAAGAGGCA 862 2503 AAAAAACUAGAUUGACUAU 538 2503 AAAAAACUAGAUUGACUAU 538 2521 AUAGUCAAUCUAGUUUUUU 863 2521 UUUAUACAAAUGGGGGCGG 539 2521 UUUAUACAAAUGGGGGCGG 539 2539 CCGCCCCCAUUUGUAUAAA 864 2539 GCUGGAAAGAGGAGAAGGA 540 2539 GCUGGAAAGAGGAGAAGGA 540 2557 UCCUUCUCCUCUUUCCAGC 865 2557 AGAGGGAGUACAAAGACAG 541 2557 AGAGGGAGUACAAAGACAG 541 2575 CUGUCUUUGUACUCCCUCU 866 2575 GGGAAUAGUGGGAUCAAAG 542 2575 GGGAAUAGUGGGAUCAAAG 542 2593 CUUUGAUCCCACUAUUCCC 867 2593 GCUAGGAAAGGCAGAAACA 543 2593 GCUAGGAAAGGCAGAAACA 543 2611 UGUUUCUGCCUUUCCUAGC 868 2611 ACAACCACUCACCAGUCCU 544 2611 ACAACCACUCACCAGUCCU 544 2629 AGGACUGGUGAGUGGUUGU 869 2629 UAGUUUUAGACCUCAUCUC 545 2629 UAGUUUUAGACCUCAUCUC 545 2647 GAGAUGAGGUCUAAAACUA 870 2647 CCAAGAUAGCAUCCCAUCU 546 2647 CCAAGAUAGCAUCCCAUCU 546 2665 AGAUGGGAUGCUAUCUUGG 871 2665 UCAGAAGAUGGGUGUUGUU 547 2665 UCAGAAGAUGGGUGUUGUU 547 2683 AACAACACCCAUCUUCUGA 872 2683 UUUCAAUGUUUUCUUUUCU 548 2683 UUUCAAUGUUUUCUUUUCU 548 2701 AGAAAAGAAAACAUUGAAA 873 2701 UGUGGUUGCAGCCUGACCA 549 2701 UGUGGUUGCAGCCUGACCA 549 2719 UGGUCAGGCUGCAACCACA 874 2719 AAAAGUGAGAUGGGAAGGG 550 2719 AAAAGUGAGAUGGGAAGGG 550 2737 CCCUUCCCAUCUCACUUUU 875 2737 GCUUAUCUAGCCAAAGAGC 551 2737 GCUUAUCUAGCCAAAGAGC 551 2755 GCUCUUUGGCUAGAUAAGC 876 2755 CUCUUUUUUAGCUCUCUUA 552 2755 CUCUUUUUUAGCUCUCUUA 552 2773 UAAGAGAGCUAAAAAAGAG 877 2773 AAAUGPAGUGCCCACUAAG 553 2773 AAAUGAAGUGCCCACUAAG 553 2791 CUUAGUGGGCACUUCAUUU 878 2791 GAAGUUCCACUUAACACAU 554 2791 GAAGUUCCACUUAACACAU 554 2809 AUGUGUUAAGUGGAACUUC 879 2809 UGAAUUUCUGCCAUAUUAA 555 2809 UGAAUUUCUGCCAUAUUAA 555 2827 UUAAUAUGGCAGAAAUUCA 880 2827 AUUUCAUUGUCUCUAUCUG 556 2827 AUUUCAUUGUCUCUAUCUG 556 2845 CAGAUAGAGACAAUGAAAU 881 2845 GAACCACCCUUUAUUCUAC 557 2845 GAACCACCCUUUAUUCUAC 557 2863 GUAGAAUAAAGGGUGGUUC 882 2863 CAUAUGAUAGGCAGCACUG 558 2863 CAUAUGAUAGGCAGCACUG 558 2881 CAGUGCUGCCUAUCAUAUG 883 2881 GAAAUAUCCUAACCCCCUA 559 2881 GAAAUAUCCUAACCCCCUA 559 2899 UAGGGGGUUAGGAUAUUUC 884 2899 AAGCUCCAGGUGCCCUGUG 560 2899 AAGCUCCAGGUGCCCUGUG 560 2917 CACAGGGCACCUGGAGCUU 885 2917 GGGAGAGCAACUGGACUAU 561 2917 GGGAGAGCAACUGGACUAU 561 2935 AUAGUCCAGUUGCUCUCCC 886 2935 UAGCAGGGCUGGGCUCUGU 562 2935 UAGCAGGGCUGGGCUCUGU 562 2953 ACAGAGCCCAGCCCUGCUA 887 2953 UCUUCCUGGUCAUAGGCUC 563 2953 UCUUCCUGGUCAUAGGCUC 563 2971 GAGCCUAUGACCAGGAAGA 888 2971 CACUCUUUCCCCCAAAUCU 564 2971 CACUCUUUCCCCCAAAUCU 564 2989 AGAUUUGGGGGAAAGAGUG 889 2989 UUCCUCUGGAGCUUUGCAG 565 2989 UUCCUCUGGAGCUUUGCAG 565 3007 CUGCAAAGCUCCAGAGGAA 890 3007 GCCAAGGUGCUAAAAGGAA 566 3007 GCCAAGGUGCUAAAAGGAA 566 3025 UUCCUUUUAGCACCUUGGC 891 3025 AUAGGUAGGAGACCUCUUC 567 3025 AUAGGUAGGAGACCUCUUC 567 3043 GAAGAGGUCUCCUACCUAU 892 3043 CUAUCUAAUCCUUAAAAGC 568 3043 CUAUCUAAUCCUUAAAAGC 568 3061 GCUUUUAAGGAUUAGAUAG 893 3061 CAUAAUGUUGAACAUUCAU 569 3061 CAUAAUGUUGAACAUUCAU 569 3079 AUGAAUGUUCAACAUUAUG 894 3079 UUCAACAGCUGAUGCCCUA 570 3079 UUCAACAGCUGAUGCCCUA 570 3097 UAGGGCAUCAGCUGUUGAA 895 3097 AUAACCCCUGCCUGGAUUU 571 3097 AUAACCCCUGCCUGGAUUU 571 3115 AAAUCCAGGCAGGGGUUAU 896 3115 UCUUCCUAUUAGGCUAUAA 572 3115 UCUUCCUAUUAGGCUAUAA 572 3133 UUAUAGCCUAAUAGGAAGA 897 3133 AGAAGUAGCAAGAUCUUUA 573 3133 AGAAGUAGCAAGAUCUUUA 573 3151 UAAAGAUCUUGCUACUUCU 898 3151 ACAUAAUUCAGAGUGGUUU 574 3151 ACAUAAUUCAGAGUGGUUU 574 3169 AAACCACUCUGAAUUAUGU 899 3169 UCAUUGCCUUCCUACCCUC 575 3169 UCAUUGCCUUCCUACCCUC 575 3187 GAGGGUAGGAAGGCAAUGA 900 3187 CUCUAAUGGCCCCUCCAUU 576 3187 CUCUAAUGGCCCCUCCAUU 576 3205 AAUGGAGGGGCCAUUAGAG 901 3205 UUAUUUGACUAAAGCAUCA 577 3205 UUAUUUGACUAAAGCAUCA 577 3223 UGAUGCUUUAGUCAAAUAA 902 3223 ACACAGUGGCACUAGCAUU 578 3223 ACACAGUGGCACUAGCAUU 578 3241 AAUGCUAGUGCCACUGUGU 903 3241 UAUACCAAGAGUAUGAGAA 579 3241 UAUACCAAGAGUAUGAGAA 579 3259 UUCUCAUACUCUUGGUAUA 904 3259 AAUACAGUGCUUUAUGGCU 580 3259 AAUACAGUGCUUUAUGGCU 580 3277 AGCCAUAAAGCACUGUAUU 905 3277 UCUAACAUUACUGCCUUCA 581 3277 UCUAACAUUACUGCCUUCA 581 3295 UGAAGGCAGUAAUGUUAGA 906 3295 AGUAUCAAGGCUGCCUGGA 582 3295 AGUAUCAAGGCUGCCUGGA 582 3313 UCCAGGCAGCCUUGAUACU 907 3313 AGAAAGGAUGGCAGCCUCA 583 3313 AGAAAGGAUGGCAGCCUCA 583 3331 UGAGGCUGCCAUCCUUUCU 908 3331 AGGGCUUCCUUAUGUCCUC 584 3331 AGGGCUUCCUUAUGUCCUC 584 3349 GAGGACAUAAGGAAGCCCU 909 3349 CCACCACAAGAGCUCCUUG 585 3349 CCACCACAAGAGCUCCUUG 585 3367 CAAGGAGCUCUUGUGGUGG 910 3367 GAUGAAGGUCAUCUUUUUC 586 3367 GAUGAAGGUCAUCUUUUUC 586 3385 GAAAAAGAUGACCUUCAUC 911 3385 CCCCUAUCCUGUUCUUCCC 587 3385 CCCCUAUCCUGUUCUUCCC 587 3403 GGGAAGAACAGGAUAGGGG 912 3403 CCUCCCCGCUCCUAAUGGU 588 3403 CCUCCCCGCUCCUAAUGGU 588 3421 ACCAUUAGGAGCGGGGAGG 913 3421 UACGUGGGUACCCAGGCUG 589 3421 UACGUGGGUACCCAGGCUG 589 3439 CAGCCUGGGUACCCACGUA 914 3439 GGUUCUUGGGCUAGGUAGU 590 3439 GGUUCUUGGGCUAGGUAGU 590 3457 ACUACCUAGCCCAAGAACC 915 3457 UGGGGACCAAGUUCAUUAC 591 3457 UGGGGACCAAGUUCAUUAC 591 3475 GUAAUGAACUUGGUCCCCA 916 3475 CCUCCCUAUCAGUUCUAGC 592 3475 CCUCCCUAUCAGUUCUAGC 592 3493 GCUAGAACUGAUAGGGAGG 917 3493 CAUAGUAAACUACGGUACC 593 3493 CAUAGUAAACUACGGUACC 593 3511 GGUACCGUAGUUUACUAUG 918 3511 CAGUGUUAGUGGGAAGAGC 594 3511 CAGUGUUAGUGGGAAGAGC 594 3529 GCUCUUCCCACUAACACUG 919 3529 CUGGGUUUUCCUAGUAUAC 595 3529 CUGGGUUUUCCUAGUAUAC 595 3547 GUAUACUAGGAAAACCCAG 920 3547 CCCACUGCAUCCUACUCCU 596 3547 CCCACUGCAUCCUACUCCU 596 3565 AGGAGUAGGAUGCAGUGGG 921 3565 UACCUGGUCAACCCGCUGC 597 3565 UACCUGGUCAACCCGCUGC 597 3583 GCAGCGGGUUGACCAGGUA 922 3583 CUUCCAGGUAUGGGACCUG 598 3583 CUUCCAGGUAUGGGACCUG 598 3601 CAGGUCCCAUACCUGGAAG 923 3601 GCUAAGUGUGGAAUUACCU 599 3601 GCUAAGUGUGGAAUUACCU 599 3619 AGGUAAUUCCACACUUAGC 924 3619 UGAUAAGGGAGAGGGAAAU 600 3619 UGAUAAGGGAGAGGGAAAU 600 3637 AUUUCCCUCUCCCUUAUCA 925 3637 UACAAGGAGGGCCUCUGGU 601 3637 UACAAGGAGGGCCUCUGGU 601 3655 ACCAGAGGCCCUCCUUGUA 926 3655 UGUUCCUGGCCUCAGCCAG 602 3655 UGUUCCUGGCCUCAGCCAG 602 3673 CUGGCUGAGGCCAGGAACA 927 3673 GCUGCCCACAAGCCAUAAA 603 3673 GCUGCCCACAAGCCAUAAA 603 3691 UUUAUGGCUUGUGGGCAGC 928 3691 ACCAAUAAAACAAGAAUAC 604 3691 ACCAAUAAAACAAGAAUAC 604 3709 GUAUUCUUGUUUUAUUGGU 929 3709 CUGAGUCAGUUUUUUAUCU 605 3709 CUGAGUCAGUUUUUUAUCU 605 3727 AGAUAAAAAACUGACUCAG 930 3727 UGGGUUCUCUUCAUUCCCA 606 3727 UGGGUUCUCUUCAUUCCCA 606 3745 UGGGAAUGAAGAGAACCCA 931 3745 ACUGCACUUGGUGCUGCUU 607 3745 ACUGCACUUGGUGCUGCUU 607 3763 AAGCAGCACCAAGUGCAGU 932 3763 UUGGCUGACUGGGAACACC 608 3763 UUGGCUGACUGGGAACACC 608 3781 GGUGUUCCCAGUCAGCCAA 933 3781 CCCAUAACUACAGAGUCUG 609 3781 CCCAUAACUACAGAGUCUG 609 3799 CAGACUCUGUAGUUAUGGG 934 3799 GACAGGAAGACUGGAGACU 610 3799 GACAGGAAGACUGGAGACU 610 3817 AGUCUCCAGUCUUCCUGUC 935 3817 UGUCCACUUCUAGCUCGGA 611 3817 UGUCCACUUCUAGCUCGGA 611 3835 UCCGAGCUAGAAGUGGACA 936 3835 AACUUACUGUGUAAAUAAA 612 3835 AACUUACUGUGUAAAUAAA 612 3853 UUUAUUUACACAGUAAGUU 937 3853 ACUUUCAGAACUGCUACCA 613 3853 ACUUUCAGAACUGCUACCA 613 3871 UGGUAGCAGUUCUGAAAGU 938 3871 AUGAAGUGAAAAUGCCACA 614 3871 AUGAAGUGAAAAUGCCACA 614 3889 UGUGGCAUUUUCACUUCAU 939 3889 AUUUUGCUUUAUAAUUUCU 615 3889 AUUUUGCUUUAUAAUUUCU 615 3907 AGAAAUUAUAAAGCAAAAU 940 3907 UACCCAUGUUGGGAAAAAC 616 3907 UACCCAUGUUGGGAAAAAC 616 3925 GUUUUUCCCAACAUGGGUA 941 3925 CUGGCUUUUUCCCAGCCCU 617 3925 CUGGCUUUUUCCCAGCCCU 617 3943 AGGGCUGGGAAAAAGCCAG 942 3943 UUUCCAGGGCAUAAAACUC 618 3943 UUUCCAGGGCAUAAAACUC 618 3961 GAGUUUUAUGCCCUGGAAA 943 3961 CAACCCCUUCGAUAGCAAG 619 3961 CAACCCCUUCGAUAGCAAG 619 3979 CUUGCUAUCGAAGGGGUUG 944 3979 GUCCCAUCAGCCUAUUAUU 620 3979 GUCCCAUCAGCCUAUUAUU 620 3997 AAUAAUAGGCUGAUGGGAC 945 3997 UUUUUUAAAGAAAACUUGC 621 3997 UUUUUUAAAGAAAACUUGC 621 4015 GCAAGUUUUCUUUAAAAAA 946 4015 CACUUGUUUUUCUUUUUAC 622 4015 CACUUGUUUUUCUUUUUAC 622 4033 GUAAAAAGAAAAACAAGUG 947 4033 CAGUUACUUCCUUCCUGCC 623 4033 CAGUUACUUCCUUCCUGCC 623 4051 GGCAGGAAGGAAGUAACUG 948 4051 CCCAAAAUUAUAAACUCUA 624 4051 CCCAAAAUUAUAAACUCUA 624 4069 UAGAGUUUAUAAUUUUGGG 949 4069 AAGUGUAAAAAAAAGUCUU 625 4069 AAGUGUAAAAAAAAGUCUU 625 4087 AAGACUUUUUUUUACACUU 950 4087 UAACAACAGCUUCUUGCUU 626 4087 UAACAACAGCUUCUUGCUU 626 4105 AAGCAAGAAGCUGUUGUUA 951 4105 UGUAAAAAUAUGUAUUAUA 627 4105 UGUAAAAAUAUGUAUUAUA 627 4123 UAUAAUACAUAUUUUUACA 952 4123 ACAUCUGUAUUUUUAAAUU 628 4123 ACAUCUGUAUUUUUAAAUU 628 4141 AAUUUAAAAAUACAGAUGU 953 4141 UCUGCUCCUGAAAAAUGAC 629 4141 UCUGCUCCUGAAAAAUGAC 629 4159 GUCAUUUUUCAGGAGCAGA 954 4159 CUGUCCCAUUCUCCACUCA 630 4159 CUGUCCCAUUCUCCACUCA 630 4177 UGAGUGGAGAAUGGGACAG 955 4177 ACUGCAUUUGGGGCCUUUC 631 4177 ACUGCAUUUGGGGCCUUUC 631 4195 GAAAGGCCCCAAAUGCAGU 956 4195 CCCAUUGGUCUGCAUGUCU 632 4195 CCCAUUGGUCUGCAUGUCU 632 4213 AGACAUGCAGACCAAUGGG 957 4213 UUUUAUCAUUGCAGGCCAG 633 4213 UUUUAUCAUUGCAGGCCAG 633 4231 CUGGCCUGCAAUGAUAAAA 958 4231 GUGGACAGAGGGAGAAGGG 634 4231 GUGGACAGAGGGAGAAGGG 634 4249 CCCUUCUCCCUCUGUCCAC 959 4249 GAGAACAGGGGUCGCCAAC 635 4249 GAGAACAGGGGUCGCCAAC 635 4267 GUUGGCGACCCCUGUUCUC 960 4267 CACUUGUGUUGCUUUCUGA 636 4267 CACUUGUGUUGCUUUCUGA 636 4285 UCAGAAAGCAACACAAGUG 961 4285 ACUGAUCCUGAACAAGAAA 637 4285 ACUGAUCCUGAACAAGAAA 637 4303 UUUCUUGUUCAGGAUCAGU 962 4303 AGAGUAACACUGAGGCGCU 638 4303 AGAGUAACACUGAGGCGCU 638 4321 AGCGCCUCAGUGUUACUCU 963 4321 UCGCUCCCAUGCACAACUC 639 4321 UCGCUCCCAUGCACAACUC 639 4339 GAGUUGUGCAUGGGAGCGA 964 4339 CUCCAAAACACUUAUCCUC 640 4339 CUCCAAAACACUUAUCCUC 640 4357 GAGGAUAAGUGUUUUGGAG 965 4357 CCUGCAAGAGUGGGCUUUC 641 4357 CCUGCAAGAGUGGGCUUUC 641 4375 GAAAGCCCACUCUUGCAGG 966 4375 CCAGGGUCUUUACUGGGAA 642 4375 CCAGGGUCUUUACUGGGAA 642 4393 UUCCCAGUAAAGACCCUGG 967 4393 AGCAGUUAAGCCCCCUCCU 643 4393 AGCAGUUAAGCCCCCUCCU 643 4411 AGGAGGGGGCUUAACUGCU 968 4411 UCACCCCUUCCUUUUUUCU 644 4411 UCACCCCUUCCUUUUUUCU 644 4429 AGAAAAAAGGAAGGGGUGA 969 4429 UUUCUUUACUCCUUUGGCU 645 4429 UUUCUUUACUCCUUUGGCU 645 4447 AGCCAAAGGAGUAAAGAAA 970 4447 UUCAAAGGAUUUUGGAAAA 646 4447 UUCAAAGGAUUUUGGAAAA 646 4465 UUUUCCAAAAUCCUUUGAA 971 4465 AGAAACAAUAUGCUUUACA 647 4465 AGAAACAAUAUGCUUUACA 647 4483 UGUAAAGCAUAUUGUUUCU 972 4483 ACUCAUUUUCAAUUUCUAA 648 4483 ACUCAUUUUCAAUUUCUAA 648 4501 UUAGAAAUUGAAAAUGAGU 973 4501 AAUUUGCAGGGGAUACUGA 649 4501 AAUUUGCAGGGGAUACUGA 649 4519 UCAGUAUCCCCUGCAAAUU 974 4519 AAAAAUACGGCAGGUGGCC 650 4519 AAAAAUACGGCAGGUGGCC 650 4537 GGCCACCUGCCGUAUUUUU 975 4537 CUAAGGCUGCUGUAAAGUU 651 4537 CUAAGGCUGCUGUAAAGUU 651 4555 AACUUUACAGCAGCCUUAG 976 4555 UGAGGGGAGAGGAAAUCUU 652 4555 UGAGGGGAGAGGAAAUCUU 652 4573 AAGAUUUCCUCUCCCCUCA 977 4573 UAAGAUUACAAGAUAAAAA 653 4573 UAAGAUUACAAGAUAAAAA 653 4591 UUUUUAUCUUGUAAUCUUA 978 4591 AACGAAUCCCCUAAACAAA 654 4591 AACGAAUCCCCUAAACAAA 654 4609 UUUGUUUAGGGGAUUCGUU 979 4609 AAAGAACAAUAGAACUGGU 655 4609 AAAGAACAAUAGAACUGGU 655 4627 ACCAGUUCUAUUGUUCUUU 980 4627 UCUUCCAUUUUGCCACCUU 656 4627 UCUUCCAUUUUGCCACCUU 656 4645 AAGGUGGCAAAAUGGAAGA 981 4645 UUCCUGUUCAUGACAGCUA 657 4645 UUCCUGUUCAUGACAGCUA 657 4663 UAGCUGUCAUGAACAGGAA 982 4663 ACUAACCUGGAGACAGUAA 658 4663 ACUAACCUGGAGACAGUAA 658 4681 UUACUGUCUCCAGGUUAGU 983 4681 ACAUUUCAUUAACCAAAGA 659 4681 ACAUUUCAUUAACCAAAGA 659 4699 UCUUUGGUUAAUGAAAUGU 984 4699 AAAGUGGGUCACCUGACCU 660 4699 AAAGUGGGUCACCUGACCU 660 4717 AGGUCAGGUGACCCACUUU 985 4717 UCUGAAGAGCUGAGUACUC 661 4717 UCUGAAGAGCUGAGUACUC 661 4735 GAGUACUCAGCUCUUCAGA 986 4735 CAGGCCACUCCAAUCACCC 662 4735 CAGGCCACUCCAAUCACCC 662 4753 GGGUGAUUGGAGUGGCCUG 987 4753 CUACAAGAUGCCAAGGAGG 663 4753 CUACAAGAUGCCAAGGAGG 663 4771 CCUCCUUGGCAUCUUGUAG 988 4771 GUCCCAGGAAGUCCAGCUC 664 4771 GUCCCAGGAAGUCCAGCUC 664 4789 GAGCUGGACUUCCUGGGAC 989 4789 CCUUAAACUGACGCUAGUC 665 4789 CCUUAAACUGACGCUAGUC 665 4807 GACUAGCGUCAGUUUAAGG 990 4807 CAAUAAACCUGGGCAAGUG 666 4807 CAAUAAACCUGGGCAAGUG 666 4825 CACUUGCCCAGGUUUAUUG 991 4825 GAGGCAAGAGAAAUGAGGA 667 4825 GAGGCAAGAGAAAUGAGGA 667 4843 UCCUCAUUUCUCUUGCCUC 992 4843 AAGAAUCCAUCUGUGAGGU 668 4843 AAGAAUCCAUCUGUGAGGU 668 4861 ACCUCACAGAUGGAUUCUU 993 4861 UGACAGGCAAGGAUGAAAG 669 4861 UGACAGGCAAGGAUGAAAG 669 4879 CUUUCAUCCUUGCCUGUCA 994 4879 GACAAAGAAGGAAAAGAGU 670 4879 GACAAAGAAGGAAAAGAGU 670 4897 ACUCUUUUCCUUCUUUGUC 995 4897 UAUCAAAGGCAGAAAGGAG 671 4897 UAUCAAAGGCAGAAAGGAG 671 4915 CUCCUUUCUGCCUUUGAUA 996 4915 GAUCAUUUAGUUGGGUCUG 672 4915 GAUCAUUUAGUUGGGUCUG 672 4933 CAGACCCAACUAAAUGAUC 997 4933 GAAAGGAAAAGUCUUUGCU 673 4933 GAAAGGAAAAGUCUUUGCU 673 4951 AGCAAAGACUUUUCCUUUC 998 4951 UAUCCGACAUGUACUGCUA 674 4951 UAUCCGACAUGUACUGCUA 674 4969 UAGCAGUACAUGUCGGAUA 999 4969 AGUACCUGUAAGCAUUUUA 675 4969 AGUACCUGUAAGCAUUUUA 675 4987 UAAAAUGCUUACAGGUACU 1000 4987 AGGUCCCAGAAUGGAAAAA 676 4987 AGGUCCCAGAAUGGAAAAA 676 5005 UUUUUCCAUUCUGGGACCU 1001 5005 AAAAAUCAGCUAUUGGUAA 677 5005 AAAAAUCAGCUAUUGGUAA 677 5023 UUACCAAUAGCUGAUUUUU 1002 5023 AUAUAAUAAUGUCCUUUCC 678 5023 AUAUAAUAAUGUCCUUUCC 678 5041 GGAAAGGACAUUAUUAUAU 1003 5041 CCUGGAGUCAGUUUUUUUA 679 5041 CCUGGAGUCAGUUUUUUUA 679 5059 UAAAAAAACUGACUCCAGG 1004 5059 AAAAAGUUAACUCUUAGUU 680 5059 AAAAAGUUAACUCUUAGUU 680 5077 AACUAAGAGUUAACUUUUU 1005 5077 UUUUACUUGUUUAAUUCUA 681 5077 UUUUACUUGUUUAAUUCUA 681 5095 UAGAAUUAAACAAGUAAAA 1006 5095 AAAAGAGAAGGGAGCUGAG 682 5095 AAAAGAGAAGGGAGCUGAG 682 5113 CUCAGCUCCCUUCUCUUUU 1007 5113 GGCCAUUCCCUGUAGGAGU 683 5113 GGCCAUUCCCUGUAGGAGU 683 5131 ACUCCUACAGGGAAUGGCC 1008 5131 UAAAGAUAAAAGGAUAGGA 684 5131 UAAAGAUAAAAGGAUAGGA 684 5149 UCCUAUCCUUUUAUCUUUA 1009 5149 AAAAGAUUCAAAGCUCUAA 685 5149 AAAAGAUUCAAAGCUCUAA 685 5167 UUAGAGCUUUGAAUCUUUU 1010 5167 AUAGAGUCACAGCUUUCCC 686 5167 AUAGAGUCACAGCUUUCCC 686 5185 GGGAAAGCUGUGACUCUAU 1011 5185 CAGGUAUAAAACCUAAAAU 687 5185 CAGGUAUAAAACCUAAAAU 687 5203 AUUUUAGGUUUUAUACCUG 1012 5203 UUAAGAAGUACAAUAAGCA 688 5203 UUAAGAAGUACAAUAAGCA 688 5221 UGCUUAUUGUACUUCUUAA 1013 5221 AGAGGUGGAAAAUGAUCUA 689 5221 AGAGGUGGAAAAUGAUCUA 689 5239 UAGAUCAUUUUCCACCUCU 1014 5239 AGUUCCUGAUAGCUACCCA 690 5239 AGUUCCUGAUAGCUACCCA 690 5257 UGGGUAGCUAUCAGGAACU 1015 5257 ACAGAGCAAGUGAUUUAUA 691 5257 ACAGAGCAAGUGAUUUAUA 691 5275 UAUAAAUCACUUGCUCUGU 1016 5275 AAAUUUGAAAUCCAAACUA 692 5275 AAAUUUGAAAUCCAAACUA 692 5293 UAGUUUGGAUUUCAAAUUU 1017 5293 ACUUUCUUAAUAUCACUUU 693 5293 ACUUUCUUAAUAUCACUUU 693 5311 AAAGUGAUAUUAAGAAAGU 1018 5311 UGGUCUCCAUUUUUCCCAG 694 5311 UGGUCUCCAUUUUUCCCAG 694 5329 CUGGGAAAAAUGGAGACCA 1019 5329 GGACAGGAAAUAUGUCCCC 695 5329 GGACAGGAAAUAUGUCCCC 695 5347 GGGGACAUAUUUCCUGUCC 1020 5347 CCCCUAACUUUCUUGCUUC 696 5347 CCCCUAACUUUCUUGCUUC 696 5365 GAAGCAAGAAAGUUAGGGG 1021 5365 CAAAAAUUAAAAUCCAGCA 697 5365 CAAAAAUUAAAAUCCAGCA 697 5383 UGCUGGAUUUUAAUUUUUG 1022 5383 AUCCCAAGAUCAUUCUACA 698 5383 AUCCCAAGAUCAUUCUACA 698 5401 UGUAGAAUGAUCUUGGGAU 1023 5401 AAGUAAUUUUGCACAGACA 699 5401 AAGUAAUUUUGCACAGACA 699 5419 UGUCUGUGCAAAAUUACUU 1024 5419 AUCUCCUCACCCCAGUGCC 700 5419 AUCUCCUCACCCCAGUGCC 700 5437 GGCACUGGGGUGAGGAGAU 1025 5437 CUGUCUGGAGCUCACCCAA 701 5437 CUGUCUGGAGCUCACCCAA 701 5455 UUGGGUGAGCUCCAGACAG 1026 5455 AGGUCACCAAACAACUUGG 702 5455 AGGUCACCAAACAACUUGG 702 5473 CCAAGUUGUUUGGUGACCU 1027 5473 GUUGUGAACCAACUGCCUU 703 5473 GUUGUGAACCAACUGCCUU 703 5491 AAGGCAGUUGGUUCACAAC 1028 5491 UAACCUUCUGGGGGAGGGG 704 5491 UAACCUUCUGGGGGAGGGG 704 5509 CCCCUCCCCCAGAAGGUUA 1029 5509 GGAUUAGCUAGACUAGGAG 705 5509 GGAUUAGCUAGACUAGGAG 705 5527 CUCCUAGUCUAGCUAAUCC 1030 5527 GACCAGAAGUGAAUGGGAA 706 5527 GACCAGAAGUGAAUGGGAA 706 5545 UUCCCAUUCACUUCUGGUC 1031 5545 AAGGGUGAGGACUUCACAA 707 5545 AAGGGUGAGGACUUCACAA 707 5563 UUGUGAAGUCCUCACCCUU 1032 5563 AUGUUGGCCUGUCAGAGCU 708 5563 AUGUUGGCCUGUCAGAGCU 708 5581 AGCUCUGACAGGCCAACAU 1033 5581 UUGAUUAGAAGCCAAGACA 709 5581 UUGAUUAGAAGCCAAGACA 709 5599 UGUCUUGGCUUCUAAUCAA 1034 5599 AGUGGCAGCAAAGGAAGAC 710 5599 AGUGGCAGCAAAGGAAGAC 710 5617 GUCUUCCUUUGCUGCCACU 1035 5617 CUUGGCCCAGGAAAAACCU 711 5617 CUUGGCCCAGGAAAAACCU 711 5635 AGGUUUUUCCUGGGCCAAG 1036 5635 UGUGGGUUGUGCUAAUUUC 712 5635 UGUGGGUUGUGCUAAUUUC 712 5653 GAAAUUAGCACAACCCACA 1037 5653 CUGUCCAGAAAAUAGGGUG 713 5653 CUGUCCAGAAAAUAGGGUG 713 5671 CACCCUAUUUUCUGGACAG 1038 5671 GGACAGAAGCUUGUGGGGU 714 5671 GGACAGAAGCUUGUGGGGU 714 5689 ACCCCACAAGCUUCUGUCC 1039 5689 UGCAUGGAGGAAUUGGGAC 715 5689 UGCAUGGAGGAAUUGGGAC 715 5707 GUCCCAAUUCCUCCAUGCA 1040 5707 CCUGGUUAUGUUGUUAUUC 716 5707 CCUGGUUAUGUUGUUAUUC 716 5725 GAAUAACAACAUAACCAGG 1041 5725 CUCGGACUGUGAAUUUUGG 717 5725 CUCGGACUGUGAAUUUUGG 717 5743 CCAAAAUUCACAGUCCGAG 1042 5743 GUGAUGUAAAACAGAAUAU 718 5743 GUGAUGUAAAACAGAAUAU 718 5761 AUAUUCUGUUUUACAUCAC 1043 5761 UUCUGUAAACCUAAUGUCU 719 5761 UUCUGUAAACCUAAUGUCU 719 5779 AGACAUUAGGUUUACAGAA 1044 5779 UGUAUAAAUAAUGAGCGUU 720 5779 UGUAUAAAUAAUGAGCGUU 720 5797 AACGCUCAUUAUUUAUACA 1045 5797 UAACACAGUAAAAUAUUCA 721 5797 UAACACAGUAAAAUAUUCA 721 5815 UGAAUAUUUUACUGUGUUA 1046 5815 AAUAAGAAGUCAAAAAAAA 722 5815 AAUAAGAAGUCAAAAAAAA 722 5833 UUUUUUUUGACUUCUUAUU 1047 5821 AAGUCAAAAAAAAAAAAAA 723 5821 AAGUCAAAAAAAAAAAAAA 723 5839 UUUUUUUUUUUUUUGACUU 1048 PSEN1NM_007319 Seq Seq Seq Pos Seq ID UPos Upper seq ID LPos Lower seq ID 3 GACAGAGUUACCUGCACCG 1049 3 GACAGAGUUACCUGCACCG 1049 21 CGGUGCAGGUAACUCUGUC 1132 21 GUUGUCCUACUUCCAGAAU 1050 21 GUUGUCCUACUUCCAGAAU 1050 39 AUUCUGGAAGUAGGACAAC 1133 39 UGCACAGAUGUCUGAGGAC 1051 39 UGCACAGAUGUCUGAGGAC 1051 57 GUCCUCAGACAUCUGUGCA 1134 57 CAACCACCUGAGCAAUACU 1052 57 CAACCACCUGAGCAAUACU 1052 75 AGUAUUGCUCAGGUGGUUG 1135 75 UAAUGACAAUAGAGAACGG 1053 75 UAAUGACAAUAGAGAACGG 1053 93 CCGUUCUCUAUUGUCAUUA 1136 93 GCAGGAGCACAACGACAGA 1054 93 GCAGGAGCACAACGACAGA 1054 111 UCUGUCGUUGUGCUCCUGC 1137 111 ACGGAGCCUUGGCCACCCU 1055 111 ACGGAGCCUUGGCCACCCU 1055 129 AGGGUGGCCAAGGCUCCGU 1138 129 UGAGCCAUUAUCUAAUGGA 1056 129 UGAGCCAUUAUCUAAUGGA 1056 147 UCCAUUAGAUAAUGGCUCA 1139 147 ACGACCCCAGGGUAACUCC 1057 147 ACGACCCCAGGGUAACUCC 1057 165 GGAGUUACCCUGGGGUCGU 1140 165 CCGGCAGGUGGUGGAGCAA 1058 165 CCGGCAGGUGGUGGAGCAA 1058 183 UUGCUCCACCACCUGCCGG 1141 183 AGAUGAGGAAGAAGAUGAG 1059 183 AGAUGAGGAAGAAGAUGAG 1059 201 CUCAUCUUCUUCCUCAUCU 1142 201 GGAGCUGACAUUGAAAUAU 1060 201 GGAGCUGACAUUGAAAUAU 1060 219 AUAUUUCAAUGUCAGCUCC 1143 219 UGGCGCCAAGCAUGUGAUC 1061 219 UGGCGCCAAGCAUGUGAUC 1061 237 GAUCACAUGCUUGGCGCCA 1144 237 CAUGCUCUUUGUCCCUGUG 1062 237 CAUGCUCUUUGUCCCUGUG 1062 255 CACAGGGACAAAGAGCAUG 1145 255 GACUCUCUGGAUGGUGGUG 1063 255 GACUCUCUGCAUGGUGGUG 1063 273 CACCACCAUGCAGAGAGUC 1146 273 GGUCGUGGCUACCAUUAAG 1064 273 GGUCGUGGCUACCAUUAAG 1064 291 CUUAAUGGUAGCCACGACC 1147 291 GUCAGUCAGCUUUUAUACC 1065 291 GUCAGUCAGCUUUUAUACC 1065 309 GGUAUAAAAGCUGACUGAC 1148 309 CCGGAAGGAUGGGCAGCUA 1066 309 CCGGAAGGAUGGGCAGCUA 1066 327 UAGCUGCCCAUCCUUCCGG 1149 327 AAUCUAUACCCCAUUCACA 1067 327 AAUCUAUACCCCAUUCACA 1067 345 UGUGAAUGGGGUAUAGAUU 1150 345 AGAAGAUACCGAGACUGUG 1068 345 AGAAGAUACCGAGACUGUG 1058 363 CACAGUCUCGGUAUCUUCU 1151 363 GGGCCAGAGAGCCCUGCAC 1069 363 GGGCCAGAGAGCCCUGCAC 1069 381 GUGCAGGGCUCUCUGGCCC 1152 381 CUCAAUUCUGAAUGCUGCC 1070 381 CUCAAUUCUGAAUGCUGCC 1070 399 GGCAGCAUUCAGAAUUGAG 1153 399 CAUCAUGAUCAGUGUCAUU 1071 399 CAUCAUGAUCAGUGUCAUU 1071 417 AAUGACACUGAUCAUGAUG 1154 417 UGUUGUCAUGACUAUCCUC 1072 417 UGUUGUCAUGACUAUCCUC 1072 435 GAGGAUAGUCAUGACAACA 1155 435 CCUGGUGGUUCUGUAUAAA 1073 435 CCUGGUGGUUCUGUAUAAA 1073 453 UUUAUACAGAACCACCAGG 1156 453 AUACAGGUGCUAUAAGGUC 1074 453 AUACAGGUGCUAUAAGGUC 1074 471 GACCUUAUAGCACCUGUAU 1157 471 CAUCCAUGCCUGGCUUAUU 1075 471 CAUCCAUGCCUGGCUUAUU 1075 489 AAUAAGCCAGGCAUGGAUG 1158 489 UAUAUCAUCUCUAUUGUUG 1076 489 UAUAUCAUCUCUAUUGUUG 1076 507 CAACAAUAGAGAUGAUAUA 1159 507 GCUGUUCUUUUUUUCAUUC 1077 507 GCUGUUCUUUUUUUCAUUC 1077 525 GAAUGAAAAAAAGAACAGC 1160 525 CAUUUACUUGGGGGAAGUG 1078 525 CAUUUACUUGGGGGAAGUG 1078 543 CACUUCCCCCAAGUAAAUG 1161 543 GUUUAAAACCUAUAACGUU 1079 543 GUUUAAAACCUAUAACGUU 1079 561 AACGUUAUAGGUUUUAAAC 1162 561 UGCUGUGGACUACAUUACU 1080 561 UGCUGUGGACUACAUUACU 1080 579 AGUAAUGUAGUCCACAGCA 1163 579 UGUUGCACUCCUGAUCUGG 1081 579 UGUUGCACUCCUGAUCUGG 1081 597 CCAGAUCAGGAGUGCAACA 1164 597 GAAUUUUGGUGUGGUGGGA 1082 597 GAAUUUUGGUGUGGUGGGA 1082 615 UCCCACCACACCAAAAUUC 1165 615 AAUGAUUUCCAUUCACUGG 1083 615 AAUGAUUUCCAUUCACUGG 1083 633 CCAGUGAAUGGAAAUCAUU 1166 633 GAAAGGUCCACUUCGACUC 1084 633 GAAAGGUCCACUUCGACUC 1084 651 GAGUCGAAGUGGACCUUUC 1167 651 CCAGCAGGCAUAUCUCAUU 1085 651 CCAGCAGGCAUAUCUCAUU 1085 669 AAUGAGAUAUGCCUGCUGG 1168 669 UAUGAUUAGUGCCCUCAUG 1086 669 UAUGAUUAGUGCCCUCAUG 1086 687 CAUGAGGGCACUAAUCAUA 1169 687 GGCCCUGGUGUUUAUCAAG 1087 687 GGCCCUGGUGUUUAUCAAG 1087 705 CUUGAUAAACACCAGGGCC 1170 705 GUACCUCCCUGAAUGGACU 1088 705 GUACCUCCCUGAAUGGACU 1088 723 AGUCCAUUCAGGGAGGUAC 1171 723 UGCGUGGCUCAUCUUGGCU 1089 723 UGCGUGGCUCAUCUUGGCU 1089 741 AGCCAAGAUGAGCCACGCA 1172 741 UGUGAUUUCGGUAUAUGAU 1090 741 UGUGAUUUCGGUAUAUGAU 1090 759 AUCAUAUACCGAAAUCACA 1173 759 UUUAGUGGCUGUUUUGUGU 1091 759 UUUAGUGGCUGUUUUGUGU 1091 777 ACACAAAACAGCCACUAAA 1174 777 UCCGAAAGGUCCACUUCGU 1092 777 UCCGAAAGGUCCACUUCGU 1092 795 ACGAAGUGGACCUUUCGGA 1175 795 UAUGCUGGUUGAAACAGCU 1093 795 UAUGCUGGUUGAAACAGCU 1093 813 AGCUGUUUCAACCAGCAUA 1176 813 UCAGGAGAGAAAUGAAACG 1094 813 UCAGGAGAGAAAUGAAACG 1094 831 CGUUUCAUUUCUCUCCUGA 1177 831 GCUUUUUCCAGCUCUCAUU 1095 831 GCUUUUUCCAGCUCUCAUU 1095 849 AAUGAGAGCUGGAAAAAGC 1178 849 UUACUCCUCAACAAUGGUG 1096 849 UUACUCCUCAACAAUGGUG 1096 867 CACCAUUGUUGAGGAGUAA 1179 867 GUGGUUGGUGAAUAUGGCA 1097 867 GUGGUUGGUGAAUAUGGCA 1097 885 UGCCAUAUUCACCAACCAC 1180 885 AGAAGGAGACCCGGAAGCU 1098 885 AGAAGGAGACCCGGAAGCU 1098 903 AGCUUCCGGGUCUCCUUCU 1181 903 UCAAAGGAGAGUAUCCAAA 1099 903 UCAAAGGAGAGUAUCCAAA 1099 921 UUUGGAUACUCUCCUUUGA 1182 921 AAAUUCCAAGUAUAAUGCA 1100 921 AAAUUCCAAGUAUAAUGCA 1100 939 UGCAUUAUACUUGGAAUUU 1183 939 AGAAAGAGCCUGUCUGCCU 1101 939 AGAAAGAGCCUGUCUGCCU 1101 957 AGGCAGACAGGCUCUUUCU 1184 957 UCCUGCUGCCAUCAACCUG 1102 957 UCCUGCUGCCAUCAACCUG 1102 975 CAGGUUGAUGGCAGCAGGA 1185 975 GCUGUCUAUAGCUCCCAUG 1103 975 GCUGUCUAUAGCUCCCAUG 1103 993 CAUGGGAGCUAUAGACAGC 1186 993 GGCACCCAGGCUGUUCAUG 1104 993 GGCACCCAGGCUGUUCAUG 1104 1011 CAUGAACAGCCUGGGUGCC 1187 1011 GCCAAAGGGUGCCUGCAGG 1105 1011 GCCAAAGGGUGCCUGCAGG 1105 1029 CCUGCAGGCACCCUUUGGC 1188 1029 GCCCACGGCACAGAAAGGG 1106 1029 GCCCACGGCACAGAAAGGG 1106 1047 CCCUUUCUGUGCCGUGGGC 1189 1047 GAGUCACAAGACACUGUUG 1107 1047 GAGUCACAAGACACUGUUG 1107 1065 CAACAGUGUCUUGUGACUC 1190 1065 GCAGAGAAUGAUGAUGGCG 1108 1065 GCAGAGAAUGAUGAUGGCG 1108 1083 CGCCAUCAUCAUUCUCUGC 1191 1083 GGGUUCAGUGAGGAAUGGG 1109 1083 GGGUUCAGUGAGGAAUGGG 1109 1101 CCCAUUCCUCACUGAACCC 1192 1101 GAAGCCCAGAGGGACAGUC 1110 1101 GAAGCCCAGAGGGACAGUC 1110 1119 GACUGUCCCUCUGGGCUUC 1193 1119 CAUCUAGGGCCUCAUCGCU 1111 1119 CAUCUAGGGCCUCAUCGCU 1111 1137 AGCGAUGAGGCCCUAGAUG 1194 1137 UCUACACCUGAGUCACGAG 1112 1137 UCUACACCUGAGUCACGAG 1112 1155 CUGGUGACUCAGGUGUAGA 1195 1155 GCUGCUGUCCAGGAACUUU 1113 1155 GCUGCUGUCCAGGAACUUU 1113 1173 AAAGUUCCUGGACAGCAGC 1196 1173 UCCAGCAGUAUCCUCGCUG 1114 1173 UCCAGCAGUAUCCUCGCUG 1114 1191 CAGCGAGGAUACUGCUGGA 1197 1191 GGUGAAGACCCAGAGGAAA 1115 1191 GGUGAAGACCCAGAGGAAA 1115 1209 UUUCCUCUGGGUCUUCACC 1198 1209 AGGGGAGUAAAACUUGGAU 1116 1209 AGGGGAGUAAAACUUGGAU 1116 1227 AUCCAAGUUUUACUCCCCU 1199 1227 UUGGGAGAUUUCAUUUUCU 1117 1227 UUGGGAGAUUUCAUUUUCU 1117 1245 AGAAAAUGAAAUCUCCCAA 1200 1245 UACAGUGUUCUGGUUGGUA 1118 1245 UACAGUGUUCUGGUUGGUA 1118 1263 UACCAACCAGAACACUGUA 1201 1263 AAAGCCUCAGCAACAGCCA 1119 1263 AAAGCCUCAGCAACAGCCA 1119 1281 UGGCUGUUGCUGAGGCUUU 1202 1281 AGUGGAGACUGGAACACAA 1120 1281 AGUGGAGACUGGAACACAA 1120 1299 UUGUGUUCCAGUCUCCACU 1203 1299 ACCAUAGCCUGUUUCGUAG 1121 1299 ACCAUAGCCUGUUUCGUAG 1121 1317 CUACGAAACAGGCUAUGGU 1204 1317 GCCAUAUUAAUUGGUUUGU 1122 1317 GCCAUAUUAAUUGGUUUGU 1122 1335 ACAAACCAAUUAAUAUGGC 1205 1335 UGCCUUACAUUAUUACUCC 1123 1335 UGCCUUACAUUAUUACUCC 1123 1353 GGAGUAAUAAUGUAAGGCA 1206 1353 CUUGCCAUUUUCAAGAAAG 1124 1353 CUUGCCAUUUUCAAGAAAG 1124 1371 CUUUCUUGAAAAUGGCAAG 1207 1371 GCAUUGCCAGCUCUUCCAA 1125 1371 GCAUUGCCAGCUCUUCCAA 1125 1389 UUGGAAGAGCUGGCAAUGC 1208 1389 AUCUCCAUCACCUUUGGGC 1126 1389 AUCUCCAUCACCUUUGGGC 1126 1407 GCCCAAAGGUGAUGGAGAU 1209 1407 CUUGUUUUCUACUUUGCCA 1127 1407 CUUGUUUUCUACUUUGCCA 1127 1425 UGGCAAAGUAGAAAACAAG 1210 1425 ACAGAUUAUCUUGUACAGC 1128 1425 ACAGAUUAUCUUGUACAGC 1128 1443 GCUGUACAAGAUAAUCUGU 1211 1443 CCUUUUAUGGACCAAUUAG 1129 1443 CCUUUUAUGGACCAAUUAG 1129 1461 CUAAUUGGUCCAUAAAAGG 1212 1461 GCAUUCCAUCAAUUUUAUA 1130 1461 GCAUUCCAUCAAUUUUAUA 1130 1479 UAUAAAAUUGAUGGAAUGC 1213 1464 UUCCAUCAAUUUUAUAUCU 1131 1464 UUCCAUCAAUUUUAUAUCU 1131 1482 AGAUAUAAAAUUGAUGGAA 1214 PSEN2 NM_000447 Seq Seq Seq Pos Seq ID UPos Upper seq ID LPos Lower seq ID 3 AGCGGCGGCGGAGCAGGCA 1215 3 AGCGGCGGCGGAGCAGGCA 1215 21 UGCCUGCUCCGCCGCCGCU 1339 21 AUUUCCAGCAGUGAGGAGA 1216 21 AUUUCCAGCAGUGAGGAGA 1216 39 UCUCCUCACUGCUGGAAAU 1340 39 ACAGCCAGAAGCAAGCUAU 1217 39 ACAGCCAGAAGCAAGCUAU 1217 57 AUAGCUUGCUUCUGGCUGU 1341 57 UUGGAGCUGAAGGAACCUG 1218 57 UUGGAGCUGAAGGAACCUG 1218 75 CAGGUUCCUUCAGCUCCAA 1342 75 GAGACAGAAGCUAGUCCCC 1219 75 GAGACAGAAGCUAGUCCCC 1219 93 GGGGACUAGCUUCUGUCUC 1343 93 CCCUCUGAAUUUUACUGAU 1220 93 CCCUCUGAAUUUUACUGAU 1220 111 AUCAGUAAAAUUCAGAGGG 1344 111 UGAAGAAACUGAGGCCACA 1221 111 UGAAGAAACUGAGGCCACA 1221 129 UGUGGCCUCAGUUUCUUCA 1345 129 AGAGCUAAAGUGACUUUUC 1222 129 AGAGCUAAAGUGACUUUUC 1222 147 GAAAAGUCACUUUAGCUCU 1346 147 CCCAAGGUCGCCCAGCGAG 1223 147 CCCAAGGUCGCCCAGCGAG 1223 165 CUCGCUGGGCGACCUUGGG 1347 165 GGACGUGGGACUUCUCAGA 1224 165 GGACGUGGGACUUCUCAGA 1224 183 UCUGAGAAGUCCCACGUCC 1348 183 ACGUCAGGAGAGUGAUGUG 1225 183 ACGUCAGGAGAGUGAUGUG 1225 201 CACAUCACUCUCCUGACGU 1349 201 GAGGGAGCUGUGUGACCAU 1226 201 GAGGGAGCUGUGUGACCAU 1226 219 AUGGUCACACAGCUCCCUC 1350 219 UAGAAAGUGACGUGUUAAA 1227 219 UAGAAAGUGACGUGUUAAA 1227 237 UUUAACACGUCACUUUCUA 1351 237 AAACCAGCGCUGCCCUCUU 1228 237 AAACCAGCGCUGCCCUCUU 1228 255 AAGAGGGCAGCGCUGGUUU 1352 255 UUGAAAGCCAGGGAGCAUC 1229 255 UUGAAAGCCAGGGAGCAUC 1229 273 GAUGCUCCCUGGCUUUCAA 1353 273 CAUUCAUUUAGCCUGCUGA 1230 273 CAUUCAUUUAGCCUGCUGA 1230 291 UCAGCAGGCUAAAUGAAUG 1354 291 AGAAGAAGAAACCAAGUGU 1231 291 AGAAGAAGAAACCAAGUGU 1231 309 ACACUUGGUUUCUUCUUCU 1355 309 UCCGGGAUUCAGACCUCUC 1232 309 UCCGGGAUUCAGACCUCUC 1232 327 GAGAGGUCUGAAUCCCGGA 1356 327 CUGCGGCCCCAAGUGUUCG 1233 327 CUGCGGCCCCAAGUGUUCG 1233 345 CGAACACUUGGGGCCGCAG 1357 345 GUGGUGCUUCCAGAGGCAG 1234 345 GUGGUGCUUCCAGAGGCAG 1234 363 CUGCCUCUGGAAGCACCAC 1358 363 GGGCUAUGCUCACAUUCAU 1235 363 GGGCUAUGCUCACAUUCAU 1235 381 AUGAAUGUGAGCAUAGCCC 1359 381 UGGCCUCUGACAGCGAGGA 1236 381 UGGCCUCUGACAGCGAGGA 1236 399 UCCUCGCUGUCAGAGGCCA 1360 399 AAGAAGUGUGUGAUGAGCG 1237 399 AAGAAGUGUGUGAUGAGCG 1237 417 CGCUCAUCACACACUUCUU 1361 417 GGACGUCCCUAAUGUCGGC 1238 417 GGACGUCCCUAAUGUCGGC 1238 435 GCCGACAUUAGGGACGUCC 1362 435 CCGAGAGCCCCACGCCGCG 1239 435 CCGAGAGCCCCACGCCGCG 1239 453 CGCGGCGUGGGGCUCUCGG 1363 453 GCUCCUGCCAGGAGGGCAG 1240 453 GCUCCUGCCAGGAGGGCAG 1240 471 CUGCCCUCCUGGCAGGAGC 1364 471 GGCAGGGCCCAGAGGAUGG 1241 471 GGCAGGGCCCAGAGGAUGG 1241 489 CCAUCCUCUGGGCCCUGCC 1365 489 GAGAGAACACUGCCCAGUG 1242 489 GAGAGAACACUGCCCAGUG 1242 507 CACUGGGCAGUGUUCUCUC 1366 507 GGAGAAGCCAGGAGAACGA 1243 507 GGAGAAGCCAGGAGAACGA 1243 525 UCGUUCUCCUGGCUUCUCC 1367 525 AGGAGGACGGUGAGGAGGA 1244 525 AGGAGGACGGUGAGGAGGA 1244 543 UCCUCCUCACCGUCCUCCU 1368 543 ACCCUGACCGCUAUGUCUG 1245 543 ACCCUGACCGCUAUGUCUG 1245 561 CAGACAUAGCGGUCAGGGU 1369 561 GUAGUGGGGUUCCCGGGCG 1246 561 GUAGUGGGGUUCCCGGGCG 1246 579 CGCCCGGGAACCCCACUAC 1370 579 GGCCGCCAGGCCUGGAGGA 1247 579 GGCCGCCAGGCCUGGAGGA 1247 597 UCCUCCAGGCCUGGCGGCC 1371 597 AAGAGCUGACCCUCAAAUA 1248 597 AAGAGCUGACCCUCAAAUA 1248 615 UAUUUGAGGGUCAGCUCUU 1372 615 ACGGAGCGAAGCACGUGAU 1249 615 ACGGAGCGAAGCACGUGAU 1249 633 AUCACGUGCUUCGCUCCGU 1373 633 UCAUGCUGUUUGUGCCUGU 1250 633 UCAUGCUGUUUGUGCCUGU 1250 651 ACAGGCACAAACAGCAUGA 1374 651 UCACUCUGUGCAUGAUCGU 1251 651 UCACUCUGUGCAUGAUCGU 1251 669 ACGAUCAUGCACAGAGUGA 1375 669 UGGUGGUAGCCACCAUCAA 1252 669 UGGUGGUAGCCACCAUCAA 1252 687 UUGAUGGUGGCUACCACCA 1376 687 AGUCUGUGCGCUUCUACAC 1253 687 AGUCUGUGCGCUUCUACAC 1253 705 GUGUAGAAGCGCACAGACU 1377 705 CAGAGAAGAAUGGACAGCU 1254 705 CAGAGAAGAAUGGACAGCU 1254 723 AGCUGUCCAUUCUUCUCUG 1378 723 UCAUCUACACGACAUUCAC 1255 723 UCAUCUACACGACAUUCAC 1255 741 GUGAAUGUCGUGUAGAUGA 1379 741 CUGAGGACACACCCUCGGU 1256 741 CUGAGGACACACCCUCGGU 1256 759 ACCGAGGGUGUGUCCUCAG 1380 759 UGGGCCAGCGCCUCCUCAA 1257 759 UGGGCCAGCGCCUCCUCAA 1257 777 UUGAGGAGGCGCUGGCCCA 1381 777 ACUCCGUGCUGAACACCCU 1258 777 ACUCCGUGCUGAACACCCU 1258 795 AGGGUGUUCAGCACGGAGU 1382 795 UCAUCAUGAUCAGCGUCAU 1259 795 UCAUCAUGAUCAGCGUCAU 1259 813 AUGACGCUGAUCAUGAUGA 1383 813 UCGUGGUUAUGACCAUCUU 1260 813 UCGUGGUUAUGACCAUCUU 1260 831 AAGAUGGUCAUAACCACGA 1384 831 UCUUGGUGGUGCUCUACAA 1261 831 UCUUGGUGGUGCUCUACAA 1261 849 UUGUAGAGCACCACCAAGA 1385 849 AGUACCGCUGCUACAAGUU 1262 849 AGUACCGCUGCUACAAGUU 1262 867 AACUUGUAGCAGCGGUACU 1386 867 UCAUCCAUGGCUGGUUGAU 1263 867 UCAUCCAUGGCUGGUUGAU 1263 885 AUCAACCAGCCAUGGAUGA 1387 885 UCAUGUCUUCACUGAUGCU 1264 885 UCAUGUCUUCACUGAUGCU 1264 903 AGCAUCAGUGAAGACAUGA 1388 903 UGCUGUUCCUCUUCACCUA 1265 903 UGCUGUUCCUCUUCACCUA 1265 921 UAGGUGAAGAGGAACAGCA 1389 921 AUAUCUACCUUGGGGAAGU 1266 921 AUAUCUACCUUGGGGAAGU 1266 939 ACUUCCCCAAGGUAGAUAU 1390 939 UGCUCAAGACCUACAAUGU 1267 939 UGCUCAAGACCUACAAUGU 1267 957 ACAUUGUAGGUCUUGAGCA 1391 957 UGGCCAUGGACUACCCCAC 1268 957 UGGCCAUGGACUACCCCAC 1268 975 GUGGGGUAGUCCAUGGCCA 1392 975 CCCUCUUGCUGACUGUCUG 1269 975 CCCUCUUGCUGACUGUCUG 1269 993 CAGACAGUCAGCAAGAGGG 1393 993 GGAACUUCGGGGCAGUGGG 1270 993 GGAACUUCGGGGCAGUGGG 1270 1011 CCCACUGCCCCGAAGUUCC 1394 1011 GCAUGGUGUGCAUCCACUG 1271 1011 GCAUGGUGUGCAUCCACUG 1271 1029 CAGUGGAUGCACACCAUGC 1395 1029 GGAAGGGCCCUCUGGUGCU 1272 1029 GGAAGGGCCCUCUGGUGCU 1272 1047 AGCACCAGAGGGCCCUUCC 1396 1047 UGCAGCAGGCCUACCUCAU 1273 1047 UGCAGCAGGCCUACCUCAU 1273 1065 AUGAGGUAGGCCUGCUGCA 1397 1065 UCAUGAUCAGUGCGCUCAU 1274 1065 UCAUGAUCAGUGCGCUCAU 1274 1083 AUGAGCGCACUGAUCAUGA 1398 1083 UGGCCCUAGUGUUCAUCAA 1275 1083 UGGCCCUAGUGUUCAUCAA 1275 1101 UUGAUGAACACUAGGGCCA 1399 1101 AGUACCUCCCAGAGUGGUC 1276 1101 AGUACCUCCCAGAGUGGUC 1276 1119 GACCACUCUGGGAGGUACU 1400 1119 CCGCGUGGGUCAUCCUGGG 1277 1119 CCGCGUGGGUCAUCCUGGG 1277 1137 CCCAGGAUGACCCACGCGG 1401 1137 GCGCCAUCUCUGUGUAUGA 1278 1137 GCGCCAUCUCUGUGUAUGA 1278 1155 UCAUACACAGAGAUGGCGC 1402 1155 AUCUCGUGGCUGUGCUGUG 1279 1155 AUCUCGUGGCUGUGCUGUG 1279 1173 CACAGCACAGCCACGAGAU 1403 1173 GUCCCAAAGGGCCUCUGAG 1280 1173 GUCCCAAAGGGCCUCUGAG 1280 1191 CUCAGAGGCCCUUUGGGAC 1404 1191 GAAUGCUGGUAGAAACUGC 1281 1191 GAAUGCUGGUAGAAACUGC 1281 1209 GCAGUUUCUACCAGCAUUC 1405 1209 CCCAGGAGAGAAAUGAGCC 1282 1209 CCCAGGAGAGAAAUGAGCC 1282 1227 GGCUCAUUUCUCUCCUGGG 1406 1227 CCAUAUUCCCUGCCCUGAU 1283 1227 CCAUAUUCCCUGCCCUGAU 1283 1245 AUCAGGGCAGGGAAUAUGG 1407 1245 UAUACUCAUCUGCCAUGGU 1284 1245 UAUACUCAUCUGCCAUGGU 1284 1263 ACCAUGGCAGAUGAGUAUA 1408 1263 UGUGGACGGUUGGCAUGGC 1285 1263 UGUGGACGGUUGGCAUGGC 1285 1281 GCCAUGCCAACCGUCCACA 1409 1281 CGAAGCUGGACCCCUCCUC 1286 1281 CGAAGCUGGACCCCUCCUC 1286 1299 GAGGAGGGGUCCAGCUUCG 1410 1299 CUCAGGGUGCCCUCCAGCU 1287 1299 CUCAGGGUGCCCUCCAGCU 1287 1317 AGCUGGAGGGCACCCUGAG 1411 1317 UCCCCUACGACCCGGAGAU 1288 1317 UCCCCUACGACCCGGAGAU 1288 1335 AUCUCCGGGUCGUAGGGGA 1412 1335 UGGAAGAAGACUCCUAUGA 1289 1335 UGGAAGAAGACUCCUAUGA 1289 1353 UCAUAGGAGUCUUCUUCCA 1413 1353 ACAGUUUUGGGGAGCCUUC 1290 1353 ACAGUUUUGGGGAGCCUUC 1290 1371 GAAGGCUCCCCAAAACUGU 1414 1371 CAUACCCCGAAGUCUUUGA 1291 1371 CAUACCCCGAAGUCUUUGA 1291 1389 UCAAAGACUUCGGGGUAUG 1415 1389 AGCCUCCCUUGACUGGCUA 1292 1389 AGCCUCCCUUGACUGGCUA 1292 1407 UAGCCAGUCAAGGGAGGCU 1416 1407 ACCCAGGGGAGGAGCUGGA 1293 1407 ACCCAGGGGAGGAGCUGGA 1293 1425 UCCAGCUCCUCCCCUGGGU 1417 1425 AGGAAGAGGAGGAAAGGGG 1294 1425 AGGAAGAGGAGGAAAGGGG 1294 1443 CCCCUUUCCUCCUCUUCCU 1418 1443 GCGUGAAGCUUGGCCUCGG 1295 1443 GCGUGAAGCUUGGCCUCGG 1295 1461 CCGAGGCCAAGCUUCACGC 1419 1461 GGGACUUCAUCUUCUACAG 1296 1461 GGGACUUCAUCUUCUACAG 1296 1479 CUGUAGAAGAUGAAGUCCC 1420 1479 GUGUGCUGGUGGGCAAGGC 1297 1479 GUGUGCUGGUGGGCAAGGC 1297 1497 GCCUUGCCCACCAGCACAC 1421 1497 CGGCUGCCACGGGCAGCGG 1298 1497 CGGCUGCCACGGGCAGCGG 1298 1515 CCGCUGCCCGUGGCAGCCG 1422 1515 GGGACUGGAAUACCACGCU 1299 1515 GGGACUGGAAUACCACGCU 1299 1533 AGCGUGGUAUUCCAGUCCC 1423 1533 UGGCCUGCUUCGUGGCCAU 1300 1533 UGGCCUGCUUCGUGGCCAU 1300 1551 AUGGCCACGAAGCAGGCCA 1424 1551 UCCUCAUUGGCUUGUGUCU 1301 1551 UCCUCAUUGGCUUGUGUCU 1301 1569 AGACACAAGCCAAUGAGGA 1425 1569 UGACCCUCCUGCUGCUUGC 1302 1569 UGACCCUCCUGCUGCUUGC 1302 1587 GCAAGCAGCAGGAGGGUCA 1426 1587 CUGUGUUCAAGAAGGCGCU 1303 1587 CUGUGUUCAAGAAGGCGCU 1303 1605 AGCGCCUUCUUGAACACAG 1427 1605 UGCCCGCCCUCCCCAUCUC 1304 1605 UGCCCGCCCUCCCCAUCUC 1304 1623 GAGAUGGGGAGGGCGGGCA 1428 1623 CCAUCACGUUCGGGCUCAU 1305 1623 CCAUCACGUUCGGGCUCAU 1305 1641 AUGAGCCCGAACGUGAUGG 1429 1641 UCUUUUACUUCUCCACGGA 1306 1641 UCUUUUACUUCUCCACGGA 1306 1659 UCCGUGGAGAAGUAAAAGA 1430 1659 ACAACCUGGUGCGGCCGUU 1307 1659 ACAACCUGGUGCGGCCGUU 1307 1677 AACGGCCGCACCAGGUUGU 1431 1677 UCAUGGACACCCUGGCCUC 1308 1677 UCAUGGACACCCUGGCCUC 1308 1695 GAGGCCAGGGUGUCCAUGA 1432 1695 CCCAUCAGCUCUACAUCUG 1309 1695 CCCAUCAGCUCUACAUCUG 1309 1713 CAGAUGUAGAGCUGAUGGG 1433 1713 GAGGGACAUGGUGUGCCAC 1310 1713 GAGGGACAUGGUGUGCCAC 1310 1731 GUGGCACACCAUGUCCCUC 1434 1731 CAGGCUGCAAGCUGCAGGG 1311 1731 CAGGCUGCAAGCUGCAGGG 1311 1749 CCCUGCAGCUUGCAGCCUG 1435 1749 GAAUUUUCAUUGGAUGCAG 1312 1749 GAAUUUUCAUUGGAUGCAG 1312 1767 CUGCAUCCAAUGAAAAUUC 1436 1767 GUUGUAUAGUUUUACACUC 1313 1767 GUUGUAUAGUUUUACACUC 1313 1785 GAGUGUAAAACUAUACAAC 1437 1785 CUAGUGCCAUAUAUUUUUA 1314 1785 CUAGUGCCAUAUAUUUUUA 1314 1803 UAAAAAUAUAUGGCACUAG 1438 1803 AAGACUUUUCUUUCCUUAA 1315 1803 AAGACUUUUCUUUCCUUAA 1315 1821 UUAAGGAAAGAAAAGUCUU 1439 1821 AAAAAUAAAGUACGUGUUU 1316 1821 AAAAAUAAAGUACGUGUUU 1316 1839 AAACACGUACUUUAUUUUU 1440 1839 UACUUGGUGAGGAGGAGGC 1317 1839 UACUUGGUGAGGAGGAGGC 1317 1857 GCCUCCUCCUCACCAAGUA 1441 1857 CAGAACCAGCUCUUUGGUG 1318 1857 CAGAACCAGCUCUUUGGUG 1318 1875 CACCAAAGAGCUGGUUCUG 1442 1875 GCCAGCUGUUUCAUCACCA 1319 1875 GCCAGCUGUUUCAUCACCA 1319 1893 UGGUGAUGAAACAGCUGGC 1443 1893 AGACUUUGGCUCCCGCUUU 1320 1893 AGACUUUGGCUCCCGCUUU 1320 1911 AAAGCGGGAGCCAAAGUCU 1444 1911 UGGGGAGCGCCUCGCUUCA 1321 1911 UGGGGAGCGCCUCGCUUCA 1321 1929 UGAAGCGAGGCGCUCCCCA 1445 1929 ACGGACAGGAAGCACAGCA 1322 1929 ACGGACAGGAAGCACAGCA 1322 1947 UGCUGUGCUUCCUGUCCGU 1446 1947 AGGUUUAUCCAGAUGAACU 1323 1947 AGGUUUAUCCAGAUGAACU 1323 1965 AGUUCAUCUGGAUAAACCU 1447 1965 UGAGAAGGUCAGAUUAGGG 1324 1965 UGAGAAGGUCAGAUUAGGG 1324 1983 CCCUAAUCUGACCUUCUCA 1448 1983 GCGGGGAGAAGAGCAUCCG 1325 1983 GCGGGGAGAAGAGCAUCCG 1325 2001 CGGAUGCUCUUCUCCCCGC 1449 2001 GGCAUGAGGGCUGAGAUGC 1326 2001 GGCAUGAGGGCUGAGAUGC 1326 2019 GCAUCUCAGCCCUCAUGCC 1450 2019 CGCAAAGAGUGUGCUCGGG 1327 2019 CGCAAAGAGUGUGCUCGGG 1327 2037 CCCGAGCACACUCUUUGCG 1451 2037 GAGUGGCCCCUGGCACCUG 1328 2037 GAGUGGCCCCUGGCACCUG 1328 2055 CAGGUGCCAGGGGCCACUC 1452 2055 GGGUGCUCUGGCUGGAGAG 1329 2055 GGGUGCUCUGGCUGGAGAG 1329 2073 CUCUCCAGCCAGAGCACCC 1453 2073 GGAAAAGCCAGUUCCCUAC 1330 2073 GGAAAAGCCAGUUCCCUAC 1330 2091 GUAGGGAACUGGCUUUUCC 1454 2091 CGAGGAGUGUUCCCAAUGC 1331 2091 CGAGGAGUGUUCCCAAUGC 1331 2109 GCAUUGGGAACACUCCUCG 1455 2109 CUUUGUCCAUGAUGUCCUU 1332 2109 CUUUGUCCAUGAUGUCCUU 1332 2127 AAGGACAUCAUGGACAAAG 1456 2127 UGUUAUUUUAUUGCCUUUA 1333 2127 UGUUAUUUUAUUGCCUUUA 1333 2145 UAAAGGCAAUAAAAUAACA 1457 2145 AGAAACUGAGUCCUGUUCU 1334 2145 AGAAACUGAGUCCUGUUCU 1334 2163 AGAACAGGACUCAGUUUCU 1458 2163 UUGUUACGGCAGUCACACU 1335 2163 UUGUUACGGCAGUCACACU 1335 2181 AGUGUGACUGCCGUAACAA 1459 2181 UGCUGGGAAGUGGCUUAAU 1336 2181 UGCUGGGAAGUGGCUUAAU 1336 2199 AUUAAGCCACUUCCCAGCA 1460 2199 UAGUAAUAUCAAUAAAUAG 1337 2199 UAGUAAUAUCAAUAAAUAG 1337 2217 CUAUUUAUUGAUAUUACUA 1461 2216 AGAUGAGUCCUGUUAGAAA 1338 2216 AGAUGAGUCCUGUUAGAAA 1338 2234 UUUCUAACAGGACUCAUCU 1462

The 3′-ends of the Upper sequence and the Lower sequence of the siNA construct can include an overhang sequence, for example about 1, 2, 3, or 4 nucleotides in length, preferably 2 nucleotides in length, wherein the overhanging sequence of the lower sequence is optionally complementary to a portion of the target sequence. The upper sequence is also referred to as the sense strand, whereas the lower sequence is also referred to as the antisense strand. The upper and lower sequences in the Table can further comprise a chemical modification having Formulae I-VII or any combination thereof. TABLE III APP, BACE, PSEN1, PSEN2, SYNTHETIC MODIFIED siNA CONSTRUCTS APP Target Seq Cmpd Seq Pos Target ID # Aliases Sequence ID 791 CAGACUAUGCAGAUGGGAGUGAA 1463 APP:793U21 sense siNA GACUAUGCAGAUGGGAGUGTT 1495 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 APP:831U21 sense siNA AGCAGAGGAGGAAGAAGUGTT 1496 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 APP:853U21 sense siNA GAGGUGGAAGAAGAAGAAGTT 1497 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 APP:1358U21 sense siNA AGAGAAUGUCCCAGGUCAUTT 1498 1568 AGAACUACAUCACCGCUCUGCAG 1467 APP:1570U21 sense siNA AACUACAUCACCGCUCUGCTT 1499 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 APP:2014U21 sense siNA UCUUUUGGGGCUGACUCUGTT 1500 2481 UGAAGUUGGACAGCAAAACCAUU 1469 APP:2483U21 sense siNA AAGUUGGACAGCAAAACCATT 1501 2482 GAAGUUGGACAGCAAAACCAUUG 1470 APP:2484U21 sense siNA AGUUGGACAGCAAAACCAUTT 1502 791 CAGACUAUGCAGAUGGGAGUGAA 1463 APP:811L21 antisense siNA CACUCCCAUCUGCAUAGUCTT 1503 (793C) 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 APP:849L21 antisense siNA CACUUCUUCCUCCUCUGCUTT 1504 (831C) 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 APP:871L21 antisense siNA CUUCUUCUUCUUCCACCUCTT 1505 (853C) 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 APP:1376L21 antisense siNA AUGACCUGGGACAUUCUCUTT 1506 (1358C) 1568 AGAACUACAUCACCGCUCUGCAG 1467 APP:1588L21 antisense siNA GCAGAGCGGUGAUGUAGUUTT 1507 (1570C) 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 APP:2032L21 antisense siNA CAGAGUCAGCCCCAAAAGATT 1508 (2014C) 2481 UGAAGUUGGACAGCAAAACCAUU 1469 APP:2501L21 antisense siNA UGGUUUUGCUGUCCAACUUTT 1509 (2483C) 2482 GAAGUUGGACAGCAAAACCAUUG 1470 APP:2502L21 antisense siNA AUGGUUUUGCUGUCCAACUTT 1510 (2484C) 791 CAGACUAUGCAGAUGGGAGUGAA 1463 APP:793U21 sense siNA stab04 B GAcuAUGCAGAUGGGAGUGTT B 1511 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 APP:831U21 sense siNA stab04 B AGcAGAGGAGGAAGAAGUGTT B 1512 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 APP:853U21 sense siNA stab04 B GAGGUGGAAGAAGAAGAAGTT B 1513 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 APP:1358U21 sense siNA stab04 B AGAGAAUGUCCCAGGUCAUTT B 1514 1568 AGAACUACAUCACCGCUCUGCAG 1467 APP:1570U21 sense siNA stab04 B AAcuAcAucAGGGCUCUGCTT B 1515 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 APP:2014U21 sense siNA stab04 B ucuuuuGGGGCUGACUCUGTT B 1516 2481 UGAAGUUGGACAGCAAAACCAUU 1469 APP:2483U21 sense siNA stab04 B AAGuuGGAcAGCAAAACcATT B 1517 2482 GAAGUUGGACAGCAAAACCAUUG 1470 APP:2484U21 sense siNA stab04 B AGuuGGACAGCAAAACCAUTT B 1518 791 CAGACUAUGCAGAUGGGAGUGAA 1463 APP:811L21 antisense siNA cAcucccAucuGcAuAGuCTsT 1519 (793C) stab05 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 APP:849L21 antisense siNA cAcuucuuccuccucuGcuTsT 1520 (831C) stab05 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 APP:871L21 antisense siNA cuucuucuucuuccAccucTsT 1521 (853C) stab05 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 APP:1376L21 antisense siNA AuGAccuGGGAcAuucucuTsT 1522 (1358C) stab05 1568 AGAACUACAUCACCGCUCUGCAG 1467 APP:1588L21 antisense siNA GcAGAGcGGuGAuGuAGuuTsT 1523 (1570C) stab05 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 APP:2032L21 antisense siNA cAGAGucAGccccAAAAGATsT 1524 (2014C) stab05 2481 UGAAGUUGGACAGCAAAACCAUU 1469 APP:2501L21 antisense siNA uGGuuuuGcuGuccAAcuuTsT 1525 (2483C) stab05 2482 GAAGUUGGACAGCAAAACCAUUG 1470 APP:2502L21 antisense siNA AuGGuuuuGcuGuccAAcuTsT 1526 (2484C) stab05 791 CAGACUAUGCAGAUGGGAGUGAA 1463 APP:793U21 sense siNA stab07 B GAcuAuGcAGAuGGGAGuGTT B 1527 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 APP:831U21 sense siNA stab07 B AGcAGAGGAGGAAGAAGuGTT B 1528 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 APP:853U21 sense siNA stab07 B GAGGuGGAAGAAGAAGAAGTT B 1529 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 APP:1358U21 sense siNA stab07 B AGAGAAuGucccAGGucAuTT B 1530 1568 AGAACUACAUCACCGCUCUGCAG 1467 APP:1570U21 sense siNA stab07 B AAcuAcAucAccGcucuGcTT B 1531 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 APP:2014U21 sense siNA stab07 B ucuuuuGGGGcuGAcucuGTT B 1532 2481 UGAAGUUGGACAGCAAAACCAUU 1469 APP:2483U21 sense siNA stab07 B AAGuuGGAcAGcAAAAccATT B 1533 2482 GAAGUUGGACAGCAAAACCAUUG 1470 APP:2484U21 sense siNA stab07 B AGuuGGAcAGcAAAAccAuTT B 1534 791 CAGACUAUGCAGAUGGGAGUGAA 1463 APP:811L21 antisense siNA cAcucccAucuGcAuAGucTsT 1535 (793C) stab11 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 APP:849L21 antisense siNA cAcuucuuccuccucuGcuTsT 1536 (831C) stab11 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 APP:871L21 antisense siNA cuucuucuucuuccAccucTsT 1537 (853C) stab11 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 APP:1376L21 antisense siNA AuGAccuGGGAcAuucucuTsT 1538 (1358C) stab11 1568 AGAACUACAUCACCGCUCUGCAG 1467 APP:1588L21 antisense siNA GcAGAGcGGuGAuGuAGuuTsT 1539 (1570C) stab11 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 APP:2032L21 antisense siNA cAGAGucAGccccAAAAGATsT 1540 (2014C) stab11 2481 UGAAGUUGGACAGCAAAACCAUU 1469 APP:2501L21 antisense siNA uGGuuuuGcuGuccAAcuuTsT 1541 (2483C) stab11 2482 GAAGUUGGACAGCAAAACCAUUG 1470 APP:2502L21 antisense siNA AuGGuuuuGcuGuccAAcuTsT 1542 (2484C) stab11 791 CAGACUAUGCAGAUGGGAGUGAA 1463 APP:793U21 sense siNA stab18 B GAcuAuGcAGAuGGGAGuGTT B 1543 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 APP:831U21 sense siNA stab18 B AGcAGAGGAGGAAGAAGuGTT B 1544 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 APP:853U21 sense siNA stab18 B GAGGuGGAAGAAGAAGAAGTT B 1545 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 APP:1358U21 sense siNA stab18 B AGAGAAuGucccAGGucAuTT B 1546 1568 AGAACUACAUCACCGCUCUGCAG 1467 APP:1570U21 sense siNA stab18 B AAcuAcAucAccGcucuGcTT B 1547 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 APP:2014U21 sense siNA stab18 B ucuuuuGGGGcuGAcucuGTT B 1548 2481 UGAAGUUGGACAGCAAAACCAUU 1469 APP:2483U21 sense siNA stab18 B AAGuuGGAcAGcAAAAccATT B 1549 2482 GAAGUUGGACAGCAAAACCAUUG 1470 APP:2484U21 sense siNA stab18 B AGuuGGAcAGcAAAAccAuTT B 1550 791 CAGACUAUGCAGAUGGGAGUGAA 1463 33885 APP:811L21 antisense siNA cAcucccAucuGcAuAGucTsT 1551 (793C) stab08 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 33886 APP:849L21 antisense siNA cAcuucuuccuccuGcuTsT 1552 (831C) stab08 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 33887 APP:871L21 antisense siNA cuucuucuucuuccAccucTsT 1553 (853C) stab08 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 33888 APP:1376L21 antisense siNA AuGAccuGGGAcAuucucuTsT 1554 (1358C) stab08 1568 AGAACUACAUCACCGCUCUGCAG 1467 33889 APP:1588L21 antisense siNA GcAGAGcGGuGAuGuAGuuTsT 1555 (1570C) stab08 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 33890 APP:2032L21 antisense siNA cAGAGucAGccccAAAAGATsT 1556 (2014C) stab08 2481 UGAAGUUGGACAGCAAAACCAUU 1469 33891 APP:2501L21 antisense siNA uGGuuuuGcuGuccAAcuuTsT 1557 (2483C) stab08 2482 GAAGUUGGACAGCAAAACCAUUG 1470 33892 APP:2502L21 antisense siNA AuGGuuuuGcuGuccAAcuTsT 1558 (2484C) stab08 791 CAGACUAUGCAGAUGGGAGUGAA 1463 33869 APP:793U21 sense siNA stab09 B GACUAUGCAGAUGGGAGUGTT B 1559 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 33870 APP:831U21 sense siNA stab09 B AGCAGAGGAGGAAGAAGUGTT B 1560 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 33871 APP:853U21 sense siNA stab09 B GAGGUGGAAGAAGAAGAAGTT B 1561 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 33872 APP:1358U21 sense siNA stab09 B AGAGAAUGUCCCAGGUCAUTT B 1562 1568 AGAACUACAUCACCGCUCUGCAG 1467 33873 APP:1570U21 sense siNA stab09 B AACUACAUCACCGCUCUGCTT B 1563 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 33874 APP:2014U21 sense siNA stab09 B UCUUUUGGGGCUGACUCUGTT B 1564 2481 UGAAGUUGGACAGCAAAACCAUU 1469 33875 APP:2483U21 sense siNA stab09 B AAGUUGGACAGCAAAACCATT B 1565 2482 GAAGUUGGACAGCAAAACCAUUG 1470 33876 APP:2484U21 sense siNA stab09 B AGUUGGACAGCAAAACCAUTT B 1566 791 CAGACUAUGCAGAUGGGAGUGAA 1463 33877 APP:811L21 antisense siNA CACUCCCAUCUGCAUAGUCTsT 1567 (793C) stab10 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 33878 APP:849L21 antisense siNA CACUUCUUCCUCCUCUGCUTsT 1568 (831C) stab10 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 33879 APP:871L21 antisense siNA CUUCUUCUUCUUCCACCUCTsT 1569 (853C) stab10 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 33880 APP:1376L21 antisense siNA AUGACCUGGGACAUUCUCUTsT 1570 (1358C) stab10 1568 AGAACUACAUCACCGCUCUGCAG 1467 33881 APP:1588L21 antisense siNA GCAGAGCGGUGAUGUAGUUTsT 1571 (1570C) stab10 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 33882 APP:2032L21 antisense siNA CAGAGUCAGCCCCAAAAGATsT 1572 (2014C) stab10 2481 UGAAGUUGGACAGCAAAACCAUU 1469 33883 APP:2501L21 antisense siNA UGGUUUUGCUGUCCAACUUTsT 1573 (2483C) stab10 2482 GAAGUUGGACAGCAAAACCAUUG 1470 33884 APP:2502L21 antiserise siNA AUGGUUUUGCUGUCCAACUTsT 1574 (2484C) stab10 791 CAGACUAUGCAGAUGGGAGUGAA 1463 APP:811L21 antisense siNA cAcucccAucuGcAuAGucTT B 1575 (793C) stab19 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 APP:849L21 antisense siNA cAcuucuuccuccucuGcuTT B 1576 (831C) stab19 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 APP:871L21 antisense siNA cuucuucuucuuccAccucTT B 1577 (853C) stab19 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 APP:1376L21 antisense siNA AuGAccuGGGAcAuucucuTT B 1578 (1358C) stab19 1568 AGAACUACAUCACCGCUCUGCAG 1467 APP:1588L21 antisense siNA GcAGAGcGGuGAuGuAGuuTT B 1579 (1570C) stab19 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 APP:2032L21 antisense siNA cAGAGucAGccccAAAAGATT B 1580 (2014C) stab19 2481 UGAAGUUGGACAGCAAAACCAUU 1469 APP:2501L21 antisense siNA uGGuuuuGcuGuccAAcuuTT B 1581 (2483C) stab19 2482 GAAGUUGGACAGCAAAACCAUUG 1470 APP:2502L21 antisense siNA AuGGuuuuGcuGuccAAcuTT B 1582 (2484C) stab19 791 CAGACUAUGCAGAUGGGAGUGAA 1463 APP:811L21 antisense siNA CACUCCCAUCUGCAUAGUCTT B 1583 (793C) stab22 829 GUAGCAGAGGAGGAAGAAGUGGC 1464 APP:849L21 antisense siNA CACUUCUU0CUCCUCUGCUTT B 1584 (831C) stab22 851 CUGAGGUGGAAGAAGAAGAAGCC 1465 APP:871L21 antisense siNA CUUCUUCUUCUUCCACCUCTT B 1585 (853C) stab22 1356 AGAGAGAAUGUCCCAGGUCAUGA 1466 APP:1376L21 antisense siNA AUGACCUGGGACAUUCUCUTT B 1586 (1358C) stab22 1568 AGAACUACAUCACCGCUCUGCAG 1467 APP:1588L21 antisense siNA GCAGAGCGGUGAUGUAGUUTT B 1587 (1570C) stab22 2012 AUUCUUUUGGGGCUGACUCUGUG 1468 APP:2032L21 antisense siNA CAGAGUCAGCCCCAAAAGATT B 1588 (2014C) stab22 2481 UGAAGUUGGACAGCAAAACCAUU 1469 APP:2501L21 antisense siNA UGGUUUUGCUGUCCAACUUTT B 1589 (2483C) stab22 2482 GAAGUUGGACAGCAAAACCAUUG 1470 APP:2502L21 antisense siNA AUGGUUUUGCUGUCCAACUTT B 1590 (2484C) stab22 BACE Target Seq Cmpd Seq Pos Target ID # Aliases Sequence ID 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1027U21 sense siNA UGGAGCCUUUCUUUGACUCTT 1591 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1030U21 sense siNA AGCCUUUCUUUGACUCUCUTT 1592 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1395U21 sense siNA AAGUUCCCUGAUGGUUUCUTT 1593 1490 AAUGGGUGAGGUUACCAACCAGU 1474 31005 BACE:1492U21 sense siNA UGGGUGAGGUUACCAACCATT 1594 1753 UCACCUUGGACAUGGAAGACUGU 1475 31006 BACE:1755U21 sense siNA ACCUUGGACAUGGAAGACUTT 1595 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1805U21 sense siNA AACCCUCAUGACCAUAGCCTT 1596 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 31007 BACE:2459U21 sense siNA UAACAUUGGUGCAAAGAUUTT 1597 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 31008 BACE:3585U21 sense siNA UGGGACCUGCUAAGUGUGGTT 1598 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1045L21 antisense siNA GAGUCAAAGAAAGGCUCCATT 1599 (1027C) 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1048L21 antisense siNA AGAGAGUCAAAGAAAGGCUTT 1600 (1030C) 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1413L21 antisense siNA AGAAACCAUCAGGGAACUUTT 1601 (1395C) 1490 AAUGGGUGAGGUUACCAACCAGU 1474 31081 BACE:1510L21 antisense siNA UGGUUGGUAACCUCACCCATT 1602 (1492C) 1753 UCACCUUGGACAUGGAAGACUGU 1475 31082 BACE:1773L21 antisense siNA AGUCUUCCAUGUCCAAGGUTT 1603 (1755C) 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1823L21 antisense siNA GGCUAUGGUCAUGAGGGUUTT 1604 (1805C) 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 31083 BACE:2477L21 antisense siNA AAUCUUUGCACCAAUGUUATT 1605 (2459C) 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 31084 BACE:3603L21 antisense siNA CCACACUUAGCAGGUCCCATT 1606 (3585C) 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1027U21 sense siNA B uGGAGccuuucuuuGAcucTT B 1607 stab04 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1030U21 sense siNA B AGccuuucuuuGAcucucuTT B 1608 stab04 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1395U21 sense siNA B AAGuucccuGAuGGuuucuTT B 1609 stab04 1490 AAUGGGUGAGGUUACCAACCAGU 1474 30729 BACE:1492U21 sense siNA B uGGGuGAGGuuAccAAccATT B 1610 stab04 1753 UCACCUUGGACAUGGAAGACUGU 1475 30730 BACE:1755U21 sense siNA B AccuuGGAcAuGGAAGAcuTT B 1611 stab04 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1805U21 sense siNA B AAcccucAuGAccAuAGccTT B 1612 stab04 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 31378 BACE:2459U21 sense siNA B uAAcAuuGGuGcAAAGAuuTT B 1613 stab04 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 30732 BACE:3585U21 sense siNA B uGGGAccuGcuAAGuGuGGTT B 1614 stab04 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1045L21 antisense siNA GAGucAAAGAAAGGcuccATsT 1615 (1027C) stab05 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1048L21 antisense siNA AGAGAGucAAAGAAAGGcuTsT 1616 (1030C) stab05 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1413L21 antisense siNA AGAAAccAucaGGGAAcuuTsT 1617 (1395C) stab05 1490 AAUGGGUGAGGUUACCAACCAGU 1474 30733 BACE:1510L21 antisense siNA uGGuuGGuAAccucAcccATsT 1618 (1492C) stab05 1753 UCACCUUGGACAUGGAAGACUGU 1475 30734 BACE:1773L21 antisense siNA AGucuuccAuGuccAAGGuTsT 1619 (1755C) stab05 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1823L21 antisense siNA GGcuAuGGucAuGAGGGuuTsT 1620 (1805C) stab05 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 31381 BACE:2477L21 antisense siNA AAucuuuGcAccAAuGuuATsT 1621 (2459C) stab05 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 30736 BACE:3603L21 antisense siNA ccAcAcuuAGcAGGucccATsT 1622 (3585C) stab05 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1027U21 sense siNA B uGGAGccuuucuuuGAcucTT B 1623 stab07 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1030U21 sense siNA B AGccuuucuuuGAcucucuTT B 1624 stab07 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1395U21 sense siNA B AAGuucccuGAuGGuuucuTT B 1625 stab07 1490 AAUGGGUGAGGUUACCAACCAGU 1474 BACE:1492U21 sense siNA B uGGGuGagguuAccAAccATT B 1626 stab07 1753 UCACCUUGGACAUGGAAGACUGU 1475 BACE:1755U21 sense siNA B AccuuGGAcAuGGAAGAcuTT B 1627 stab07 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1805U21 sense siNA B AAcccucAuGAccAuAGccTT B 1628 stab07 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 31384 BACE:2459U21 sense siNA B uAAcAuuGGuGcAAAGAuuTT B 1629 stab07 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 BACE:3585U21 sense siNA B uGGGAccuGcuAAGuGuGGTT 8 1630 stab07 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1045L21 antisense siNA GAGucAAAGAAAGGcuccATsT 1631 (1027C) stab11 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1048L21 antisense siNA AGAGAGucAAAGAAAGGucTsT 1632 (1030C) stab11 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1413L21 antisense siNA AGAAAccAucAGGGAAcuuTsT 1633 (1395C) stab11 1490 AAUGGGUGAGGUUACCAACCAGU 1474 BACE:1510L21 antisense siNA uGGuuGGuAAccucAcccATsT 1634 (1492C) stab11 1753 UCACCUUGGACAUGGAAGACUGU 1475 BACE:1 773L21 antisense siNA AGucuuccAuGuccAAGGuTsT 1635 (1755C) stab11 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1823L21 antisense siNA GGcuAuGGucAuGAGGGuuTsT 1636 (1805C) stab11 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 31387 BACE:2477L21 antisense siNA AAucuuuGcAccAAuGuuATsT 1637 (2459C) stab11 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 BACE:3603L21 antisense siNA ccAcAcuuAGcAGGuccATsT 1638 (3585C) stab11 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1027U21 sense siNA B uGGAGccuuucuuuGAcucTT B 1639 stab18 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1030U21 sense siNA B AGccuuucuuuGAcucucuTT B 1640 stab18 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1395U21 sense siNA B AAGuucccuGAuGGuuucuTT B 1641 stab18 1490 AAUGGGUGAGGUUACCAACCAGU 1474 BACE:1492U21 sense siNA B uGGGuGAGGuuAccAAccATT B 1642 stab18 1753 UCACCUUGGACAUGGAAGACUGU 1475 BACE:1755U21 sense siNA B AccuuGGAcAuGGAAGAcuTT B 1643 stab18 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1805U21 sense siNA B AAcccucAuGAccAuAGccTT B 1644 stab18 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 BACE:2459U21 sense siNA B uAAcAuuGGuGcAAAGAuuTT B 1645 stab18 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 BACE:3585U21 sense siNA B uGGGAccuGcuAAGuGuGGTT B 1646 stab18 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1045L21 antisense siNA GAGucAAAGAAAGGucuuATsT 1647 (1027C) stab08 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1048L21 antisense siNA AGAGAGucAAAGAAAGGcuTsT 1648 (1030C) stab08 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1413L21 antisense siNA AGAAAccAucAGGGAAcuuTsT 1649 (1395C) stab08 1490 AAUGGGUGAGGUUACCAACCAGU 1474 BACE:1510L21 antisense siNA uGGuuGGuAAccucAcccATsT 1650 (1492C) stab08 1753 UCACCUUGGACAUGGAAGACUGU 1475 BACE:1773L21 antisense siNA AGucuuccAuGuccAAGGuTsT 1651 (1755C) stab08 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1823L21 antisense siNA GGcuAuGGucAuGAGGGuuTsT 1652 (1805C) stab08 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 BACE:2477L21 antisense siNA AAucuuuGcAccAAuGuuATsT 1653 (2459C) stab08 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 BACE:3603L21 antisense siNA ccAcAcuuAGcAGGucccATsT 1654 (3585C) stab08 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1027U21 sense siNA B UGGAGCCUUUCUUUGACUCTT B 1655 stab09 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1030U21 sense siNA B AGCCUUUCUUUGACUCUCUTT B 1656 stab09 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1395U21 sense siNA B AAGUUCCCUGAUGGUUUCUTT B 1657 stab09 1490 AAUGGGUGAGGUUACCAACCAGU 1474 BACE:1492U21 sense siNA B UGGGUGAGGUUACCAACCATT B 1658 stab09 1753 UCACCUUGGACAUGGAAGACUGU 1475 BACE:1755U21 sense siNA B ACCUUGGACAUGGAAGACUTT B 1659 stab09 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1805U21 sense siNA B AACCCUCAUGACCAUAGCCTT B 1660 stab09 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 BACE:2459U21 sense siNA B UAACAUUGGUGCAAAGAUUTT B 1661 stab09 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 BACE:3585U21 sense siNA B UGGGACCUGCUAAGUGUGGTT B 1662 stab09 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1045L21 antisense siNA GAGUCAAAGAAAGGCUCCATsT 1663 (1027C) stab10 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1048L21 antisense siNA AGAGAGUCAAAGAAAGGCUTsT 1664 (1030C) stab10 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1413L21 antisense siNA AGAAACCAUCAGGGAACUUTsT 1665 (1395C) stab10 1490 AAUGGGUGAGGUUACCAACCAGU 1474 BACE:1510L21 antisense siNA UGGUUGGUAACCUCACCCATsT 1666 (1492C) stab10 1753 UCACCUUGGACAUGGAAGACUGU 1475 BACE:1773L21 antisense siNA AGUCUUCCAUGUCCAAGGUTsT 1667 (1755C) stab10 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1823L21 antisense siNA GGCUAUGGUCAUGAGGGUUTsT 1668 (1805C) stab10 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 BACE:2477L21 antisense siNA AAUCUUUGCACCAAUGUUATsT 1669 (2459C) stab10 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 BACE:3603L21 antisense siNA CCACACUUAGCAGGUCCCATsT 1670 (3585C) stab10 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1045L21 antisense siNA GAGucAAAGAAAGGcuccATT B 1671 (1027C) stab19 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1048L21 antisense siNA AGAGAGucAAAGAAAGGcuTT B 1672 (1030C) stab19 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1413L21 antisense siNA AGAAAccAucAGGGAAcuuTT B 1673 (1395C) stab19 1490 AAUGGGUGAGGUUACCAACCAGU 1474 BACE:1510L21 antisense siNA uGGuuGGuAAccucAcccATT B 1674 (1492C) stab19 1753 UCACCUUGGACAUGGAAGACUGU 1475 BACE:1773L21 antisense siNA AGucuuccAuGuccAAGGuTT B 1675 (1755C) stab19 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1823L21 antisense siNA GGcuAuGGucAuGAGGGuuTT B 1676 (1805C) stab19 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 BACE:2477L21 antisense siNA AAucuuuGcAccAAuGuuATT B 1677 (2459C) stab19 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 BACE:3603L21 antisense siNA ccAcAcuuAGcAGGucccATT B 1678 (3585C) stab19 1025 CCUGGAGCCUUUCUUUGACUCUC 1471 BACE:1045L21 antisense siNA GAGUCAAAGAAAGGCUCCATT B 1679 (1027C) stab22 1028 GGAGCCUUUCUUUGACUCUCUGG 1472 BACE:1048L21 antisense siNA AGAGAGUCAAAGAAAGGCUTT B 1680 (1030C) stab22 1393 AGAAGUUCCCUGAUGGUUUCUGG 1473 BACE:1413L21 antisense siNA AGAAACCAUCAGGGAACUUTT B 1681 (1395C) stab22 1490 AAUGGGUGAGGUUACCAACCAGU 1474 BACE:1510L21 antisense siNA UGGUUGGUAACCUCACCCATT 8 1682 (1492C) stab22 1753 UCACCUUGGACAUGGAAGACUGU 1475 BACE:1773L21 antisense siNA AGUCUUCCAUGUCCAAGGUTT B 1683 (1755C) stab22 1803 UCAACCCUCAUGACCAUAGCCUA 1476 BACE:1823L21 antisense siNA GGCUAUGGUCAUGAGGGUUTT B 1684 (1805C) stab22 2457 CCUAACAUUGGUGCAAAGAUUGC 1477 BACE:2477L21 antisense siNA AAUCUUUGCACCAAUGUUATT B 1685 (2459C) stab22 3583 UAUGGGACCUGCUAAGUGUGGAA 1478 BACE:3603L21 antisense siNA CCACACUUAGCAGGUCCCATT B 1686 (3585C) stab22 2457 CCUAACAUUGGUGCAAAGAUUGC 657 31390 BACE:2459U21 sense siNA inv B uuAGAAACGuGGUUACAAUTT B 1687 stab04 2457 CCUAACAUUGGUGCAAAGAUUGC 657 31393 BACE:2477L21 antisense siNA AuuGuAAccAcGuuucuAATsT 1688 (2459C) inv stab05 2457 CCUAACAUUGGUGCAAAGAUUGC 657 31396 BACE:2459U21 sense siNA inv B uuAGAAAcGuGGuuAcAAuTT B 1689 stab07 2457 CCUAACAUUGGUGCAAAGAUUGC 657 31399 BACE:2477L21 antisense siNA AuuGuAAccAcGuuucuAATsT 1690 (2459C) inv stab11 PSEN1 Target Seq Cmpd Seq Pos Target ID # Aliases Sequence ID 693 CUAAUGGACGACCCCAGGGUAAC 1479 PSEN1:695U21 sense siNA AAUGGACGACCCCAGGGUATT 1691 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 PSEN1:1133U21 sense siNA GUUGCACUCCUGAUCUGGATT 1692 1493 GAAAGCACAGAAAGGGAGUCACA 1481 PSEN1:1495U21 sense siNA AAGCACAGAAAGGGAGUCATT 1693 1505 AGGGAGUCACAAGACACUGUUGC 1482 PSEN1:1507LL21 sense siNA GGAGUCACAAGACACUGUUTT 1694 1748 GACUGGAACACAACCAUAGCCUG 1483 PSEN1:1750U21 sense siNA CUGGAACACAACCAUAGCCU 1695 1751 UGGAACACAACCAUAGCCUGUUU 1484 PSEN1:1753U21 sense siNA GAACACAACCAUAGCCUGUTT 1696 2184 CUACCAGAUUUGAGGGACGAGGU 1485 PSEN1:2186U21 sense siNA ACCAGAUUUGAGGGACGAGTT 1697 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 PSEN1:3009U21 sense siNA UAUGCCCAAAGCGGUAGAATT 1698 693 CUAAUGGACGACCCCAGGGUAAC 1479 PSEN1:713L21 antisense siNA UACCCUGGGGUCGUCCAUUTT 1699 (695C) 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 PSEN1:1151L21 antisense siNA UCCAGAUCAGGAGUGCAACTT 1700 (1133C) 1493 GAAAGCACAGAAAGGGAGUCACA 1481 PSEN1:1513L21 antisense siNA UGACUCCCUUUCUGUGCUUTT 1701 (1495C) 1505 AGGGAGUCACAAGACACUGUUGC 1482 PSEN1:1525L21 antisense siNA AACAGUGUCUUGUGACUCCTT 1702 (1507C) 1748 GACUGGAACACAACCAUAGCCUG 1483 PSEN1:1768L21 antisense siNA GGCUAUGGUUGUGUUCCAGTT 1703 (1750C) 1751 UGGAACACAACCAUAGCCUGUUU 1484 PSEN1:1771L21 antisense siNA ACAGGCUAUGGUUGUGUUCTT 1704 (1753C) 2184 CUACCAGAUUUGAGGGACGAGGU 1485 PSEN1:2204L21 antisense siNA CUCGUCCCUCAAAUCUGGUTT 1705 (2186C) 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 PSEN1:3027L21 antisense siNA UUCUACCGCUUUGGGCAUATT 1706 (3009C) 693 CUAAUGGACGACCCCAGGGUAAC 1479 PSEN1:695U21 sense siNA B AAuGGAcGAccccAGGGuATT B 1707 stab04 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 PSEN1:1133U21 sense siNA B GuuGcAcuccuGAucuGGATT B 1708 stab04 1493 GAAAGCACAGAAAGGGAGUCACA 1481 PSEN1:1495U21 sense siNA B AAGcAcAGAAAGGGAGucATT B 1709 stab04 1505 AGGGAGUCACAAGACACUGUUGC 1482 PSEN1:1507U21 sense siNA B GGAGucAcAAGAcAcuGuuTT B 1710 stab04 1748 GACUGGAACACAACCAUAGCCUG 1483 PSEN1:1750U21 sense siNA B cuGGAAcAcAAccAuAGccTT B 1711 stab04 1751 UGGAACACAACCAUAGCCUGUUU 1484 PSEN1:1753U21 sense siNA B GAAcAcAAccAuAGccuGuTT B 1712 stab04 2184 CUACCAGAUUUGAGGGACGAGGU 1485 PSEN1:2186U21 sense siNA B AccAGAuuuGAGGGAcGAGTT B 1713 stab04 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 PSEN1:3009U21 sense siNA B uAuGcccAAAGcGGuAGAATT B 1714 stab04 693 CUAAUGGACGACCCCAGGGUAAC 1479 PSEN1:713L21 antisense siNA uAcccuGGGucGuccAuuTsT 1715 (695C) stab05 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 PSEN1:1151L21 antisense siNA uccAGAucAGGAGuGcAAcTsT 1716 (1133C) stab05 1493 GAAAGCACAGAAAGGGAGUCACA 1481 PSEN1:1513L21 antisense siNA uGAcucccuuucuGuGcuuTsT 1717 (1495C) stab05 1505 AGGGAGUCACAAGACACUGUUGC 1482 PSEN1:1525L21 antisense siNA AAcAGuGucuuGuGAcuccTsT 1718 (1507C) stab05 1748 GACUGGAACACAACCAUAGCCUG 1483 PSEN1:1768L21 antisense siNA GGcuAuGGuuGuGuuccAGTsT 1719 (1750C) stab05 1751 UGGAACACAACCAUAGCCUGUUU 1484 PSEN1:1771L21 antisense siNA AcAGGcuAuGGuuGuGuucTsT 1720 (1753C) stab05 2184 CUACCAGAUUUGAGGGACGAGGU 1485 PSEN1:2204L21 antisense siNA cucGucccucAAAucuGGuTsT 1721 (2186C) stab05 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 PSEN1:3027L21 antisense siNA uucuAccGcuuuGGGcAuATsT 1722 (3009C) stab05 693 CUAAUGGACGACCCCAGGGUAAC 1479 PSEN1:695U21 sense siNA B AAuGGAcGAccccAGGGuATT B 1723 stab07 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 PSEN1:1133U21 sense siNA B GuuGcAcuccuGAucuGGATT B 1724 stab07 1493 GAAAGCACAGAAAGGGAGUCACA 1481 PSEN1:1495U21 sense siNA B AAGcAcAGAAAGGGAGucATT B 1725 stab07 1505 AGGGAGUCACAAGACACUGUUGC 1482 PSEN1:1507U21 sense siNA B GGAGucAcAAGAcAcuGuuTT B 1726 stab07 1748 GACUGGAACACAACCAUAGCCUG 1483 PSEN1:1750U21 sense siNA B cuGGAAcAcAAccAuAGccTT B 1727 stab07 1751 UGGAACACAACCAUAGCCUGUUU 1484 PSEN1:1753U21 sense siNA B GAAcAcAAccAuAGccuGuTT B 1728 stab07 2184 CUACCAGAUUUGAGGGACGAGGU 1485 PSEN1:2186U21 sense siNA B AccAGAuuuGAGGGAcGAGTT B 1729 stab07 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 PSEN1:3009U21 sense siNA B uAuGcccAAAGcGGuAGAATT B 1730 stab07 693 CUAAUGGACGACCCCAGGGUAAC 1479 PSEN1:713L21 antisense siNA uAcccuGGGGucGuccAuuTsT 1731 (695C) stab11 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 PSEN1:1151L21 antisense siNA uccAGAucAGGAGuGcAAcTsT 1732 (1133C) stab11 1493 GAAAGCACAGAAAGGGAGUCACA 1481 PSEN1:1513L21 antisense siNA uGAcucccuuucuGuGcuuTsT 1733 (1495C) stab11 1505 AGGGAGUCACAAGACACUGUUGC 1482 PSEN1:1525L21 antisense siNA AAcAGuGucuuGuGAcuccTsT 1734 (1507C) stab11 1748 GACUGGAACACAACCAUAGCCUG 1483 PSEN1:1768L21 antisense siNA GGcuAuGGuuGuGuuccAGTsT 1735 (1750C) stab11 1751 UGGAACACAACCAUAGCCUGUUU 1484 PSEN1:1771L21 antisense siNA AcAGGcuAuGGuuGuGuucTsT 1736 (1753C) stab11 2184 CUACCAGAUUUGAGGGACGAGGU 1485 PSEN1:2204L21 antisense siNA cucGucccucAAAucuGGuTsT 1737 (2186C) stab11 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 PSEN1:3027L21 antisense siNA uucuAccGcuuuGGGcAuATsT 1738 (3009C) stab11 693C UAAUGGACGACCCCAGGGUAAC 1479 PSEN1:695U21 sense siNA B AAuGGAcGAccccAGGGuATT B 1739 stab18 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 PSEN1:1133U21 sense siNA B GuuGcAcuccuGAucuGGATT B 1740 stab18 1493 GAAAGCACAGAAAGGGAGUCACA 1481 PSEN1:1495U21 sense siNA B AAGcAcAGAAAGGGAGucATT B 1741 stab18 1505 AGGGAGUCACAAGACACUGUUGC 1482 PSEN1:1507U21 sense siNA B GGAGucAcAAGAcAcuGuuTT B 1742 stab18 1748 GACUGGAACACAACCAUAGCCUG 1483 PSEN1:1750U21 sense siNA B cuGGAAcAcAAccAuAGccTT B 1743 stab18 1751 UGGAACACAACCAUAGCCUGUUU 1484 PSEN1:1753U21 sense siNA B GAAcAcAAccAuAGccuGuTT B 1744 stab18 2184 CUACCAGAUUUGAGGGACGAGGU 1485 PSEN1:2186U21 sense siNA B AccAGAuuuGAGGGAcGAGTT B 1745 stab18 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 PSEN1:3009U21 sense siNA B uAuGCccAAAGCGGuAGAATT B 1746 stab18 693 CUAAUGGACGACCCCAGGGUAAC 1479 33933 PSEN1:713L21 antisense siNA uAcccuGGGGucGuccAuuTsT 1747 (695C) stab08 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 33934 PSEN1:1151L21 antisense siNA uccAGAucAGGAGuGcAAcTsT 1748 (1133C) stab08 1493 GAAAGCACAGAAAGGGAGUCACA 1481 33935 PSEN1:1513L21 antisense siNA uGAcucccuuucuGuGcuuTsT 1749 (1495C) stab08 1505 AGGGAGUCACAAGACACUGUUGC 1482 33936 PSEN1:1525L21 antisense siNA AAcAGuGucuuGuGAcuccTsT 1750 (1507C) stab08 1748 GACUGGAACACAACCAUAGCCUG 1483 33937 PSEN1:1768L21 antisense siNA GGcuAuGGuuGuGuuccAGTsT 1751 (1750C) stab08 1751 UGGAACACAACCAUAGCCUGUUU 1484 33938 PSEN1:1771L21 antisense siNA AcAGGcuAuGGuuGuGuucTsT 1752 (1753C) stab08 2184 CUACCAGAUUUGAGGGACGAGGU 1485 33939 PSEN1:2204L21 antisense siNA cucGucccucAAAucuGGuTsT 1753 (2186C) stab08 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 33940 PSEN1:3027L21 antisense siNA uucuAccGcuuuGGGcAuATsT 1754 (3009C) stab08 693 CUAAUGGACGACCCCAGGGUAAC 1479 33917 PSEN1:695U21 sense siNA B AAUGGACGACCCCAGGGUATT B 1755 stab09 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 33918 PSEN1:1133U21 sense siNA B GUUGCACUCCUGAUCUGGATT B 1756 stab09 1493 GAAAGCACAGAAAGGGAGUCACA 1481 33919 PSEN1:1495U21 sense siNA B AAGCACAGAAAGGGAGUCATT B 1757 stab09 1505 AGGGAGUCACAAGACACUGUUGC 1482 33920 PSEN1:1507U21 sense siNA B GGAGUCACAAGACACUGUUTT B 1758 stab09 1748 GACUGGAACACAACCAUAGCCUG 1483 33921 PSEN1:1750U21 sense siNA B CUGGAACACAACCAUAGCCTT B 1759 stab09 1751 UGGAACACAACCAUAGCCUGUUU 1484 33922 PSEN1:1753U21 sense siNA B GAACACAACCAUAGCCUGUTT B 1760 stab09 2184 CUACCAGAUUUGAGGGACGAGGU 1485 33923 PSEN1:2186U21 sense siNA B ACCAGAUUUGAGGGACGAGTT B 1761 stab09 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 33924 PSEN1:3009U21 sense siNA B UAUGCCCAAAGCGGUAGAATT B 1762 stab09 693 CUAAUGGACGACCCCAGGGUAAC 1479 33925 PSEN1:713L21 antisense siNA UACCCUGGGGUCGUCCAUUTsT 1763 (695C) stab10 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 33926 PSEN1:1151L21 antisense siNA UCCAGAUCAGGAGUGCAACTsT 1764 (1133C) stab10 1493 GAAAGCACAGAAAGGGAGUCACA 1481 33927 PSEN1:1513L21 antisense siNA UGACUCCCUUUCUGUGCUUTsT 1765 (1495C) stab10 1505 AGGGAGUCACAAGACACUGUUGC 1482 33928 PSEN1:1525L21 antisense siNA AACAGUGUCUUGUGACUCCTsT 1766 (1507C) stab10 1748 GACUGGAACACAACCAUAGCCUG 1483 33929 PSEN1:1768L21 antisense siNA GGCUAUGGUUGUGUUCCAGTsT 1767 (1750C) stab10 1751 UGGAACACAACCAUAGCCUGUUU 1484 33930 PSEN1:1771L21 antisense siNA ACAGGCUAUGGUUGUGUUCTsT 1768 (1753C) stab10 2184 CUACCAGAUUUGAGGGACGAGGU 1485 33931 PSEN1:2204L21 antisense siNA CUCGUCCCUCAAAUCUGGUTsT 1769 (2186C) stab10 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 33932 PSEN1:3027L21 antisense siNA UUCUACCGCUUUGGGCAUATsT 1770 (3009C) stab10 693 CUAAUGGACGACCCCAGGGUAAC 1479 PSEN1:713L21 antisense siNA uAcccuGGGGucGuccAuuTT B 1771 (695C) stab19 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 PSEN1:1151L21 antisense siNA uccAGAucAGGAGuGcAAcTT B 1772 (1133C) stab19 1493 GAAAGCACAGAAAGGGAGUCACA 1481 PSEN1:1513L21 antisense siNA uGAcucccuuucuGuGcuuTT B 1773 (1495C) stab19 1505 AGGGAGUCACAAGACACUGUUGC 1482 PSEN1:1525L21 antisense siNA AAcAGuGucuuGuGAcuccTT B 1774 (1507C) stab19 1748 GACUGGAACACAACCAUAGCCUG 1483 PSEN1:1768L21 antisense siNA GGcuAuGGuuGuGuuccAGTT B 1775 (1750C) stab19 1751 UGGAACACAACCAUAGCCUGUUU 1484 PSEN1:1771L21 antisense siNA AcAGGcuAuGGuuGuGuucTT B 1776 (1753C) stab19 2184 CUACCAGAUUUGAGGGACGAGGU 1485 PSEN1:2204L21 antisense siNA cucGucccucAAAucuGGuTT B 1777 (2186C) stab19 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 PSEN1:3027L21 antisense siNA uucuAccGcuuuGGGcAuATT B 1778 (3009C) stab19 693 CUAAUGGACGACCCCAGGGUAAC 1479 PSEN1:713L21 antisense siNA UACCCUGGGGUCGUCCAUUTT B 1779 (695C) stab22 1131 CUGUUGCACUCCUGAUCUGGAAU 1480 PSEN1:1151L21 antisense siNA UCCAGAUCAGGAGUGCAACTT B 1780 (1133C) stab22 1493 GAAAGCACAGAAAGGGAGUCACA 1481 PSEN1:1513L21 antisense siNA UGACUCCCUUUCUGUGCUUTT B 1781 (1495C) stab22 1505 AGGGAGUCACAAGACACUGUUGC 1482 PSEN1:1525L21 antisense siNA AACAGUGUCUUGUGACUCCTT B 1782 (1507C) stab22 1748 GACUGGAACACAACCAUAGCCUG 1483 PSEN1:1768L21 antisense siNA GGCUAUGGUUGUGUUCCAGTT B 1783 (1750C) stab22 1751 UGGAACACAACCAUAGCCUGUUU 1484 PSEN1:1771L21 antisense siNA ACAGGCUAUGGUUGUGUUCTT B 1784 (1753C) stab22 2184 CUACCAGAUUUGAGGGACGAGGU 1485 PSEN1:2204L21 antisense siNA CUCGUCCCUCAAAUCUGGUTT B 1785 (2186C) stab22 3007 UGUAUGCCCAAAGCGGUAGAAUU 1486 PSEN1:3027L21 antisense siNA UUCUACCGCUUUGGGCAUATT B 1786 (3009C) stab22 PSEN2 Target Seq Cmpd Seq Pos Target ID # Aliases Sequence ID 104 UUACUGAUGAAGAAACUGAGGCC 1487 PSEN2:106U21 sense siNA ACUGAUGAAGAAACUGAGGTT 1787 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 PSEN2:262U21 sense siNA CCAGGGAGCAUCAUUCAUUTT 1788 549 ACCGCUAUGUCUGUAGUGGGGUU 1489 PSEN2:551U21 sense siNA CGCUAUGUCUGUAGUGGGGTT 1789 597 AAGAGCUGACCCUCAAAUACGGA 1490 PSEN2:599U21 sense siNA GAGCUGACCCUCAAAUACGTT 1790 730 CACGACAUUCACUGAGGACACAC 1491 PSEN2:732U21 sense siNA CGACAUUCACUGAGGACACTT 1791 938 GUGCUCAAGACCUACAAUGUGGC 1492 PSEN2:940U21 sense siNA GCUCAAGACCUACAAUGUGTT 1792 947 ACCUACAAUGUGGCCAUGGACUA 1493 PSEN2:949U21 sense siNA CUACAAUGUGGCCAUGGACTT 1793 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 PSEN2:2097U21 sense siNA GUGUUCCCAAUGCUUUGUCTT 1794 104 UUACUGAUGAAGAAACUGAGGCC 1487 PSEN2:124L21 antisense siNA CCUCAGUUUCUUCAUCAGUTT 1795 (106C) 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 PSEN2:280L21 antisense siNA AAUGAAUGAUGCUCCCUGGTT 1796 (262C) 549 ACCGCUAUGUCUGUAGUGGGGUU 1489 PSEN2:569L21 antisense siNA CCCCACUACAGACAUAGCGTT 1797 (551C) 597 AAGAGCUGACCCUCAAAUACGGA 1490 PSEN2:617L21 antisense siNA CGUAUUUGAGGGUCAGCUCTT 1798 (599C) 730 CACGACAUUCACUGAGGACACAC 1491 PSEN2:750L21 antisense siNA GUGUCCUCAGUGAAUGUCGTT 1799 (732C) 938 GUGCUCAAGACCUACAAUGUGGC 1492 PSEN2:958L21 antisense siNA CACAUUGUAGGUCUUGAGCTT 1800 (940C) 947 ACCUACAAUGUGGCCAUGGACUA 1493 PSEN2:967L21 antisense siNA GUCCAUGGCCACAUUGUAGTT 1801 (949C) 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 PSEN2:2115L21 antisense siNA GACAAAGCAUUGGGAACACTT 1802 (2097C) 104 UUACUGAUGAAGAAACUGAGGCC 1487 PSEN2:106U21 sense siNA B AcuGAUGAAGAAAcuGAGGTT B 1803 stab04 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 PSEN2:262U21 sense siNA B ccAGGGAGcAucAuucAuuTT B 1804 stab04 549 ACCGCUAUGUCUGUAGUGGGGUU 1489 PSEN2:551U21 sense siNA B cGcuAuGucuGuAGuGGGGTT B 1805 stab04 597 AAGAGCUGACCCUCAAAUACGGA 1490 PSEN2:599U21 sense siNA B GAGcuGAcccucAAAuAcGTT B 1806 stab04 730 CACGACAUUCACUGAGGACACAC 1491 PSEN2:732U21 sense siNA B cGAcAuucAcuGAGGAcAcTT B 1807 stab04 938 GUGCUCAAGACCUACAAUGUGGC 1492 PSEN2:940U21 sense siNA B GcucAAGAccuAcAAuGuGTT B 1808 stab04 947 ACCUACAAUGUGGCCAUGGACUA 1493 PSEN2:949U21 sense siNA B cuAcAAuGuGGccAuGGAcTT B 1809 stab04 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 PSEN2:2097U21 sense siNA B GuGuucccAAuGcuuuGucTT B 1810 stab04 104 UUACUGAUGAAGAAACUGAGGCC 1487 PSEN2:124L21 antisense siNA ccucAGuuucuucAucAGuTsT 1811 (106C) stab05 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 PSEN2:280L21 antisense siNA AAuGAAuGAuGcucccuGGTsT 1812 (262C) stab05 549 ACCGCUAUGUCUGUAGUGGGGUU 1489 PSEN2:569L21 antisense siNA ccccAcuAcAGAcAuAGcGTsT 1813 (551C) stab05 597 AAGAGCUGACCCUCAAAUACGGA 1490 PSEN2:617L21 antisense siNA cGuAuuuGAGGGucAGcucTsT 1814 (599C) stab05 730 CACGACAUUCACUGAGGACACAC 1491 PSEN2:750L21 antisense siNA GuGuccucAGuGAAuGucGTsT 1815 (732C) stab05 938 GUGCUCAAGACCUACAAUGUGGC 1492 PSEN2:958L21 antisense siNA cAcAuuGuAGGucuuGAGcTsT 1816 (940C) stab05 947 ACCUACAAUGUGGCCAUGGACUA 1493 PSEN2:967L21 antisense siNA GuccAuGGccAcAuuGuAGTsT 1817 (949C) stab05 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 PSEN2:2115L21 antisense siNA GAcAAAGcAuuGGGAAcAcTsT 1818 (2097C) stab05 104 UUACUGAUGAAGAAACUGAGGCC 1487 PSEN2:106U21 sense siNA B AcuGAuGAAGAAAcuGAGGTT B 1819 stab07 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 PSEN2:262U21 sense siNA B ccAGGGAGcAucAAuucAuuTT B 1820 stab07 549 ACCGCUAUGUCUGUAGUGGGGUU 1489 PSEN2:551U21 sense siNA B cGcuAuGucuGuAGuGGGGTT B 1821 stab07 597 AAGAGCUGACCCUCAAAUACGGA 1490 PSEN2:599U21 sense siNA B GAGcuGAcccucAAAuAcGTT B 1822 stab07 730 CACGACAUUCACUGAGGACACAC 1491 PSEN2:732U21 sense siNA B cGAcAuucaAcuGAGGAcAcTT B 1823 stab07 938 GUGCUCAAGACCUACAAUGUGGC 1492 PSEN2:940U21 sense siNA B GcucAAGAccuAcAAuGuGTT B 1824 stab07 947 ACCUACAAUGUGGCCAUGGACUA 1493 PSEN2:949U21 sense siNA B cuAcAAuGuGGccAuGGAcTT B 1825 stab07 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 PSEN2:2097U21 sense siNA B GuGuucccAAuGcuuuGucTT B 1826 stab07 104 UUACUGAUGAAGAAACUGAGGCC 1487 PSEN2:124L21 antisense siNA ccucAGuuucuucAucAGuTsT 1827 (106C) stab11 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 PSEN2:280L21 antisense siNA AAuGAAuGAuGcucccuGGTsT 1828 (262C) stab11 549 ACCGCUAUGUCUGUAGUGGGGUU 1489 PSEN2:569L21 antisense siNA ccccAcuAcAGAcAuAGcGTsT 1829 (551C) stab11 597 AAGAGCUGACCCUCAAAUACGGA 1490 PSEN2:617L21 antisense siNA cGuAuuuGAGGGucAGcucTsT 1830 (599C) stab11 730 CACGACAUUCACUGAGGACACAC 1491 PSEN2:750L21 antisense siNA GuGuccucAGuGAAuGucGTsT 1831 (732C) stab11 938 GUGCUCAAGACCUACAAUGUGGC 1492 pSEN2:958L21 antisense siNA cAcAuuGuAGGucuuGAGcTsT 1832 (940C) stab11 947 ACCUACAAUGUGGCCAUGGACUA 1493 PSEN2:967L21 antisense siNA GuccAuGGccAcAuuGuAGTsT 1833 (949C) stab11 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 PSEN2:2115L21 antisense siNA GAcAAAGcAuuGGGAAcAcTsT 1834 (2097C) stab11 104 UUACUGAUGAAGAAACUGAGGCC 1487 PSEN2:106U21 sense siNA B AcuGAuGAAGAAAcuGAGGTT B 1835 stab18 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 PSEN2:262U21 sense siNA B ccAGGGAGcAucAuucAuuTT B 1836 stab18 549 ACCGCUAUGUCUGUAGUGGGGUU 1489 PSEN2:551U21 sense siNA B cGcuAuGucuGuAGuGGGGTT B 1837 stab18 597 AAGAGCUGACCCUCAAAUACGGA 1490 PSEN2:599U21 sense siNA B GAGcuGAcccucAAAuAcGTT B 1838 stab18 730 CACGACAUUCACUGAGGACACAC 1491 PSEN2:732U21 sense siNA B cGAcAuucAcuGAGGAcAcTT B 1839 stab18 938 GUGCUCAAGACCUACAAUGUGGC 1492 PSEN2:940U21 sense siNA B GcucAAGAccuAcAAuGuGTT B 1840 stab18 947 ACCUACAAUGUGGCCAUGGACUA 1493 PSEN2:949U21 sense siNA B cuAcAAuGuGGccAuGGAcTT B 1841 stab18 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 PSEN2:2097U21 sense siNA B GuGuucccAAuGcuuuGucTT B 1842 stab18 104 UUACUGAUGAAGAAACUGAGGCC 1487 33957 PSEN2:124L21 antisense siNA ccucAGuuucuucAucAGuTsT 1843 (106C) stab08 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 33958 PSEN2:280L21 antisense siNA AAuGAAuGAuGcucccuGGTsT 1844 (262C) stab08 549 ACCGCUAUGUCUGUAGUGGGGUU 1489 33959 PSEN2:569L21 antisense siNA cccAcuAcAGAcAuAGcGTsT 1845 (551C) stab08 597 AAGAGCUGACCCUCAAAUACGGA 1490 33960 PSEN2:617L21 antisense siNA cGuAuuuGAGGGucAGcucTsT 1846 (599C) stab08 730 CACGACAUUCACUGAGGACACAC 1491 33961 PSEN2:750L21 antisense siNA GuGuccucAGuGAAuGucGTsT 1847 (732C) stab08 938 GUGCUCAAGACCUACAAUGUGGC 1492 33962 PSEN2:958L21 antisense siNA cAcAuuGuAGGucuuGAGcTsT 1848 (940C) stab08 947 ACCUACAAUGUGGCCAUGGACUA 1493 33963 PSEN2:967L21 antisense siNA GuccAuGGccAcAuuGuAGTsT 1849 (949C) stab08 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 33964 PSEN2:2115L21 antisense siNA GAcAAAGcAuuGGGAAcAcTsT 1850 (2097C) stab08 104 UUACUGAUGAAGAAACUGAGGCC 1487 33941 PSEN2:106U21 sense siNA B ACUGAUGAAGAAACUGAGGTT B 1851 stab09 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 33942 PSEN2:262U21 sense siNA B CCAGGGAGCAUCAUUCAUUTT B 1852 stab09 549 ACCGCUAUGUCUGUAGUGGGGUU 1489 33943 PSEN2:551U21 sense siNA B CGCUAUGUCUGUAGUGGGGTT B 1853 stab09 597 AAGAGCUGACCCUCAAAUACGGA 1490 33944 PSEN2:599U21 sense siNA B GAGCUGACCCUCAAAUACGTT B 1854 stab09 730 CACGACAUUCACUGAGGACACAC 1491 33945 PSEN2:732U21 sense siNA B CGACAUUCACUGAGGACACTT B 1855 stab09 938 GUGCUCAAGACCUACAAUGUGGC 1492 33946 PSEN2:940U21 sense siNA B GCUCAAGACCUACAAUGUGTT B 1856 stab09 947 ACCUACAAUGUGGCCAUGGACUA 1493 33947 PSEN2:949U21 sense siNA B CUACAAUGUGGCCAUGGACTT B 1857 stab09 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 33948 PSEN2:2097U21 sense siNA B GUGUUCCCAAUGCUUUGUCTT B 1858 stab09 104 UUACUGAUGAAGAAACUGAGGCC 1487 33949 PSEN2:124L21 antisense siNA CCUCAGUUUCUUCAUCAGUTsT 1859 (106C) stab10 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 33950 PSEN2:280L21 antisense siNA AAUGAAUGAUGCUCCCUGGTsT 1860 (262C) stab10 549 ACCGCUAUGUCUGUAGUGGGGUU 1489 33951 PSEN2:569L21 antisense siNA CCCCACUACAGACAUAGCGTsT 1861 (551C) stab10 597 AAGAGCUGACCCUCAAAUACGGA 1490 33952 PSEN2:617L21 antisense siNA CGUAUUUGAGGGUCAGCUCTsT 1862 (599C) stab10 730 CACGACAUUCACUGAGGACACAC 1491 33953 PSEN2:750L21 antisense siNA GUGUCCUCAGUGAAUGUCGTsT 1863 (732C) stab10 938 GUGCUCAAGACCUACAAUGUGGC 1492 33954 PSEN2:958L21 antisense siNA CACAUUGUAGGUCUUGAGCTsT 1864 (940C) stab10 947 ACCUACAAUGUGGCCAUGGACUA 1493 33955 PSEN2:967L21 antisense siNA GUCCAUGGCCACAUUGUAGTsT 1865 (949C) stab10 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 33956 PSEN2:2115L21 antisense siNA GACAAAGCAUUGGGAACACTsT 1866 (2097C) stab10 104 UUACUGAUGAAGAAACUGAGGCC 1487 PSEN2:124L21 antisense siNA ccucAGuuucuucAucAGuTT B 1867 (106C) stab19 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 PSEN2:280L21 antisense siNA AAuGAAuGAuGcucccuGGTT B 1868 (262C) stab19 549 ACCGCUAUGUCUGUAGUGGGGUU 1469 PSEN2:569L21 antisense siNA ccccAcuAcAGAcAuAGcGTT B 1869 (551C) stab19 597 AAGAGCUGACCCUCAAAUACGGA 1490 PSEN2:617L21 antisense siNA cGuAuuuGAGGGucAGcucTT B 1870 (599C) stab19 730 CACGACAUUCACUGAGGACACAC 1491 PSEN2:750L21 antisense siNA GuGuccucAGuGAAuGucGTT B 1871 (732C) stab19 938 GUGCUCAAGACCUACAAUGUGGC 1492 PSEN2:958L21 antisense siNA cAcAuuGuAGGucuuGAGcTT B 1872 (940C) stab19 947 ACCUACAAUGUGGCCAUGGACUA 1493 PSEN2:967L21 antisense siNA GuccAuGGccAcAuuGuAGTT B 1873 (949C) stab19 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 PSEN2:2115L21 antisense siNA GAcAAAGcAuuGGGAAcAcTT B 1874 (2097C) stab19 104 UUACUGAUGAAGAAACUGAGGCC 1487 PSEN2:124L21 antisense siNA CCUCAGUUUCUUCAUCAGUTT B 1875 (106C) stab22 260 AGCCAGGGAGCAUCAUUCAUUUA 1488 PSEN2:280L21 antisense siNA AAUGAAUGAUGCUCCCUGGTT B 1876 (262C) stab22 549 ACCGCUAUGUCUGUAGUGGGGUU 1489 PSEN2:569L21 antisense siNA CCCCACUACAGACAUAGCGTT B 1877 (551C) stab22 597 AAGAGCUGACCCUCAAAUACGGA 1490 PSEN2:617L21 antisense siNA CGUAUUUGAGGGUCAGCUCTT B 1878 (599C) stab22 730 CACGACAUUCACUGAGGACACAC 1491 PSEN2:750L21 antisense siNA GUGUCCUCAGUGAAUGUCGTT B 1879 (732C) stab22 938 GUGCUCAAGACCUACAAUGUGGC 1492 PSEN2:958L21 antisense siNA CACAUUGUAGGUCUUGAGCTT B 1880 (940C) stab22 947 ACCUACAAUGUGGCCAUGGACUA 1493 PSEN2:967L21 antisense siNA GUCCAUGGCCACAUUGUAGTT B 1881 (949C) stab22 2095 GAGUGUUCCCAAUGCUUUGUCCA 1494 PSEN2:2115L21 antisense siNA GACAAAGCAUUGGGAACACTT B 1882 (2097C) stab22 Uppercase = ribonucleotide u,c = 2′-deoxy-2′-fluoro U,C T = thymidine B = inverted deoxy abasic s = phosphorothioate linkage A = deoxy Adenosine G = deoxy Guanosine G = 2′-O-methyl Guanosine A 2′-O-methyl Adenosine

TABLE IV Non-limiting examples of Stabilization Chemistries for chemically modified siNA constructs Chemistry pyrimidine Purine cap p = S Strand “Stab 00” Ribo Ribo TT at S/AS 3′-ends “Stab 1” Ribo Ribo — 5 at 5′-end S/AS 1 at 3′-end “Stab 2” Ribo Ribo — All Usually AS linkages “Stab 3” 2′-fluoro Ribo — 4 at 5′-end Usually S 4 at 3′-end “Stab 4” 2′-fluoro Ribo 5′ and — Usually S 3′-ends “Stab 5” 2′-fluoro Ribo — 1 at 3′-end Usually AS “Stab 6” 2′-O- Ribo 5′ and — Usually S Methyl 3′-ends “Stab 7” 2′-fluoro 2′-deoxy 5′ and — Usually S 3′-ends “Stab 8” 2′-fluoro 2′-O- — 1 at 3′-end Usually AS Methyl “Stab 9” Ribo Ribo 5′ and — Usually S 3′-ends “Stab 10” Ribo Ribo — 1 at 3′-end Usually AS “Stab 11” 2′-fluoro 2′-deoxy — 1 at 3-end Usually AS “Stab 12” 2′-fluoro LNA 5′ and Usually S 3′-ends “Stab 13” 2′-fluoro LNA 1 at 3′-end Usually AS “Stab 14” 2′-fluoro 2′-deoxy 2 at 5′-end Usually AS 1 at 3′-end “Stab 15” 2′-deoxy 2′-deoxy 2 at 5′-end Usually AS 1 at 3′-end “Stab 16” Ribo 2′-O- 5′ and Usually S Methyl 3′-ends “Stab 17” 2′-O- 2′-O- 5′ and Usually S Methyl Methyl 3′-ends “Stab 18” 2′-fluoro 2′-O- 5′ and Usually S Methyl 3′-ends “Stab 19” 2′-fluoro 2′-O- 3′-end Usually AS Methyl “Stab 20” 2′-fluoro 2′-deoxy 3′-end Usually AS “Stab 21” 2′-fluoro Ribo 3′-end Usually AS “Stab 22” Ribo Ribo 3′-end - Usually AS “Stab 23” 2′-fluoro* 2′-deoxy* 5′ and Usually S 3′-ends “Stab 24” 2′-fluoro* 2′-O- — 1 at 3′-end Usually AS Methyl* “Stab 25” 2′-fluoro* 2′-O- — 1 at 3′-end Usually AS Methyl* CAP = any terminal cap, see for example FIG. 10. All Stab 00-25 chemistries can comprise 3′-terminal thymidine (TT) residues All Stab 00-25 chemistries typically comprise about 21 nucleotides, but can vary as described herein. S = sense strand AS = antisense strand *Stab 23 has single ribonucleotide adjacent to 3′-CAP *Stab 24 has single ribonucleotide at 5′-terminus *Stab 25 has three ribonucleotides at 5′-terminus

TABLE V Wait Time* Reagent Equivalents Amount Wait Time* DNA 2′-O-methyl Wait Time* RNA A. 2.5 μmol Synthesis Cycle ABI 394 Instrument Phosphoramidites 6.5 163 μL 45 sec 2.5 min 7.5 min S-Ethyl Tetrazole 23.8 238 μL 45 sec 2.5 min 7.5 min Acetic Anhydride 100 233 μL 5 sec 5 sec 5 sec N-Methyl Imidazole 186 233 μL 5 sec 5 sec 5 sec TCA 176 2.3 mL 21 sec 21 sec 21 sec Iodine 11.2 1.7 mL 45 sec 45 sec 45 sec Beaucage 12.9 645 μL 100 sec 300 sec 300 sec Acetonitrile NA 6.67 mL NA NA NA B. 0.2 μmol Synthesis Cycle ABI 394 Instrument Phosphoramidites 15 31 μL 45 sec 233 sec 465 sec S-Ethyl Tetrazole 38.7 31 μL 45 sec 233 min 465 sec Acetic Anhydride 655 124 μL 5 sec 5 sec 5 sec N-Methyl Imidazole 1245 124 μL 5 sec 5 sec 5 sec TCA 700 732 μL 10 sec 10 sec 10 sec Iodine 20.6 244 μL 15 sec 15 sec 15 sec Beaucage 7.7 232 μL 100 sec 300 sec 300 sec Acetonitrile NA 2.64 mL NA NA NA C. 0.2 μmol Synthesis Cycle 96 well Instrument Equivalents: Amount: Wait Time* DNA/2′-O- DNA/2′-O- Wait Time* 2′-O- Wait Time* Reagent methyl/Ribo methyl/Ribo DNA methyl Ribo Phosphoramidites 22/33/66 40/60/120 μL 60 sec 180 sec 360 sec S-Ethyl Tetrazole 70/105/210 40/60/120 μL 60 sec 180 min 360 sec Acetic Anhydride 265/265/265 50/50/50 μL 10 sec 10 sec 10 sec N-Methyl Imidazole 502/502/502 50/50/50 μL 10 sec 10 sec 10 sec TCA 238/475/475 250/500/500 μL 15 sec 15 sec 15 sec Iodine 6.8/6.8/6.8 80/80/80 μL 30 sec 30 sec 30 sec Beaucage 34/51/51 80/120/120 100 sec 200 sec 200 sec Acetonitrile NA 1150/1150/1150 μL NA NA NA *Wait time does not include contact time during delivery. *Tandem synthesis utilizes double coupling of linker molecule 

1. A chemically synthesized double stranded short interfering nucleic acid (siNA) molecule that directs cleavage of an amyloid precursor protein (APP)RNA via RNA interference (RNAi), wherein: a. each strand of said siNA molecule is about 18 to about 23 nucleotides in length; and b. one strand of said siNA molecule comprises nucleotide sequence having sufficient complementarity to said APP RNA for the siNA molecule to direct cleavage of the APP RNA via RNA interference.
 2. The siNA molecule of claim 1, wherein said siNA molecule comprises no ribonucleotides.
 3. The siNA molecule of claim 1, wherein said siNA molecule comprises one or more ribonucleotides.
 4. The siNA molecule of claim 1, wherein one strand of said double-stranded siNA molecule comprises a nucleotide sequence that is complementary to a nucleotide sequence of a APP gene or a portion thereof, and wherein a second strand of said double-stranded siNA molecule comprises a nucleotide sequence substantially similar to the nucleotide sequence or a portion thereof of said APP RNA.
 5. The siNA molecule of claim 4, wherein each strand of the siNA molecule comprises about 18 to about 23 nucleotides, and wherein each strand comprises at least about 19 nucleotides that are complementary to the nucleotides of the other strand.
 6. The siNA molecule of claim 1, wherein said siNA molecule comprises an antisense region comprising a nucleotide sequence that is complementary to a nucleotide sequence of a APP gene or a portion thereof, and wherein said siNA further comprises a sense region, wherein said sense region comprises a nucleotide sequence substantially similar to the nucleotide sequence of said APP gene or a portion thereof.
 7. The siNA molecule of claim 6, wherein said antisense region and said sense region comprise about 18 to about 23 nucleotides, and wherein said antisense region comprises at least about 18 nucleotides that are complementary to nucleotides of the sense region.
 8. The siNA molecule of claim 1, wherein said siNA molecule comprises a sense region and an antisense region, and wherein said antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by a APP gene, or a portion thereof, and said sense region comprises a nucleotide sequence that is complementary to said antisense region.
 9. The siNA molecule of claim 6, wherein said siNA molecule is assembled from two separate oligonucleotide fragments wherein one fragment comprises the sense region and a second fragment comprises the antisense region of said siNA molecule.
 10. The siNA molecule of claim 6, wherein said sense region is connected to the antisense region via a linker molecule.
 11. The siNA molecule of claim 10, wherein said linker molecule is a polynucleotide linker.
 12. The siNA molecule of claim 10, wherein said linker molecule is a non-nucleotide linker.
 13. The siNA molecule of claim 6, wherein pyrimidine nucleotides in the sense region are 2′-O-methyl pyrimidine nucleotides.
 14. The siNA molecule of claim 6, wherein purine nucleotides in the sense region are 2′-deoxy purine nucleotides.
 15. The siNA molecule of claim 6, wherein pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides.
 16. The siNA molecule of claim 9, wherein the fragment comprising said sense region includes a terminal cap moiety at a 5′-end, a 3′-end, or both of the 5′ and 3′ ends of the fragment comprising said sense region.
 17. The siNA molecule of claim 16, wherein said terminal cap moiety is an inverted deoxy abasic moiety.
 18. The siNA molecule of claim 6, wherein pyrimidine nucleotides of said antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides.
 19. The siNA molecule of claim 6, wherein purine nucleotides of said antisense region are 2′-O-methyl purine nucleotides.
 20. The siNA molecule of claim 6, wherein purine nucleotides present in said antisense region comprise 2′-deoxy-purine nucleotides.
 21. The siNA molecule of claim 18, wherein said antisense region comprises a phosphorothioate internucleotide linkage at the 3′ end of said antisense region.
 22. The siNA molecule of claim 6, wherein said antisense region comprises a glyceryl modification at a 3′ end of said antisense region.
 23. The siNA molecule of claim 9, wherein each of the two fragments of said siNA molecule comprise about 21 nucleotides.
 24. The siNA molecule of claim 23, wherein about 19 nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule and wherein at least two 3′ terminal nucleotides of each fragment of the siNA molecule are not base-paired to the nucleotides of the other fragment of the siNA molecule.
 25. The siNA molecule of claim 24, wherein each of the two 3′ terminal nucleotides of each fragment of the siNA molecule are 2′-deoxy-pyrimidines.
 26. The siNA molecule of claim 25, wherein said 2′-deoxy-pyrimidine is 2′-deoxy-thymidine.
 27. The siNA molecule of claim 23, wherein all of the about 21 nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule.
 28. The siNA molecule of claim 23, wherein about 19 nucleotides of the antisense region are base-paired to the nucleotide sequence of the RNA encoded by a APP gene or a portion thereof.
 29. The siNA molecule of claim 23, wherein about 21 nucleotides of the antisense region are base-paired to the nucleotide sequence of the RNA encoded by a APP gene or a portion thereof.
 30. The siNA molecule of claim 9, wherein a 5′-end of the fragment comprising said antisense region optionally includes a phosphate group.
 31. A composition comprising the siNA molecule of claim 1 in an pharmaceutically acceptable carrier or diluent.
 32. A siNA according to claim 1 wherein the APP RNA comprises Genbank Accession No. NM_(—)000484.
 33. A siNA according to claim 1 wherein said siNA comprises any of SEQ ID NOs. 1-199, 200-398, 1463-1470, and 1495-1590.
 34. A composition comprising the siNA of claim 32 together with a pharmaceutically acceptable carrier or diluent.
 35. A composition comprising the siNA of claim 33 together with a pharmaceutically acceptable carrier or diluent. 